Gathering and Secondary Skills Tradeskilling FAQ.
So, you want to know how to use those herbalism and mining points? Or your secondary skills? Then read on, friend!
First of all, because of the wonder of Blizzard balance, you will want to start your skills as early as possible. You could start at level one, if you wanted to. This is because the things you can gather at low levels will be found in the low level zones. Once you get to higher skills, you should be of sufficient level to go to higher zones for the more advanced items. Contrary-wise, if you wait until you are level 30 to start herbalism, you will find yourself forced back into a newbie zone, trying to farm your low level herbs, fish, and metals before you can go back to your high zones and pick up that iron or mageroyal!
Each character can take up to five skills: two primary and three secondary.
Primary skills are as follows:
Of the primary skills, several are linked. Mining is a gathering skill that procures the metals and rocks needed for blacksmithing and engineering. Herbalism is a skill that gathers the herbs needed for alchemy. Skinning strips animals of leather used in leatherworking and tailoring. Leatherworking makes leather items, tailoring makes cloth items. Enchanting uses green-named (magical) items, to put magical properties on armor of all kinds. 
In my guild, we are aiming at getting two volunteers for each of the crafting-type primaries (blacksmithing, tailoring, engineering, leatherworking, alchemy, with ONE dedicated enchanter, with as many other gatherers and secondaries as players wish to have. This is so we don't have, for example, five blacksmiths struggling to each get enough copper/tin/bronze to get their levels up. Instead, with only two for each manufacturing profession, our gatherers will know who to give the copper to, and there will be more copper for them to level up quickly.
Well, if you play a class that can only wear mail, for example, you'd probably be better off taking mining and blacksmithing as opposed to skinning and tailoring. On the other hand, you might have people in your guild that have a lot of time on their hands, and you might want to gather things for them to skill up with, and have them make it for you!
I'm sure there are lots of guides for the regular manufacturing skills. Instead, we'll discuss the gathering professions of herbalism and mining, of the primaries, and the three secondary professions.
Your first step is to find a trainer. To do so, you will need to find a guard, one with a chat bubble on the arrow when you mouse over him. When you click him, he will ask you what you are looking for. Tell him you are looking for a profession trainer. Sometimes you will be lucky and the trainer will be in your city. Other times, you will have to travel to a different city first. For example, in order for a human to pick up mining, you would have to travel to the Dwarven District in Stormwind. Herbalism can be found in the Mage Quarter. To fish, a human would go to the dock at Crystal Lake, right behind the Lion's Pride Inn. The first aid trainer is called a Physician and can be found upstairs of Lion's Pride Inn and a cook can be found in the kitchen. Once you have located your trainer, click on him. He will have a set of options. You want to begin with Apprentice. Highlight apprentice, and click "Train now". Sometimes a trainer does not have any options at until you tell him you want to "train now". Before you go merrily off on your way, however, don't forget to train the recipes he has for you! For mining, these include smelting the ores. First Aid will give you recipes for making your first bandages, and cooking will give you some simple recipes.
Each of these professions needs different tools:
You can use any fire in any town for this, from cozy fires to cooking fires to the Dwarven braziers in Ironforge. You will know that you are close enough to a fire when your cooking icon lights up. When you are in the wilderness, you may make your own fire, without materials now as of patch 3.1.
All you need is cloth to make the specific bandages in your inventory.
You WILL need to equip your fishing pole. You do not need bait, but if you buy attractors like Shiny Baubles or nightcrawlers, you will get a boost to your fishing skill for 5-10 minutes. This will not affect your ability to skill-up, but will affect the types of things you can catch, and the locations at which you can fish. For example, you will need a skill of around 75 before you can fish in Lakeshire, and you will want a good lure (+75 or more) to ensure that you can fish most of the time instead of letting the fish get away.
But I do like to take out a little pet and have it run around with me as I collect flowers, to keep me company!
This can be purchased at very low cost at a craft seller, like the one at the cart next to the blacksmithing building in Goldshire. You do not need to equip the pick, just keep it in your inventory. 
Prospecting is a subskill of jewelcrafting and does not require a specialized tool. It does require a stack of 5 of the same type of ore however to attempt to find gems within the stack. The ore is consumed in the process.
To skin your kills, you will need to purchase a skinning knife or a gnomish pocketknife from a merchant. You are not required to equip this to skin your kills, you simply need to have it in your bags. There are also different dropped weapons that can double as a skinning knife, such as Finkle's Skinner, available from The Beast in the Blackrock Spire.
First things first. Get set up. Click on your spellbook, and go to your abilities tab. In among your racial and profession traits, you will see the icons for your new tradeskills. For mining, you will have two abilities: mining and smelting. Cooking has two: cooking and building fires. Fishing, herbalism, and first aid will all have only one icon. Drag each icon down to your hotbar. If you use the Cosmos UI, I suggest putting all skills on one bar. If you don't, then use the arrows to the right of your single row of hotkeys to select a fresh hotbar, and put mining/herbalism on the new bar, with as many defensive/soloing spells or abilities as you feel comfortable with. If you have chosen both mining and herbalism, you will be selecting both, so you will definitely want them together, but you will also not want to impair your ability to defend yourself if that gold dot takes you into a gnoll lair. Set it up however it most comfortable for you, however.
Yes. For herbalism or mining, click the Herbalism or mining icon. You will see a small circle on the upper left hand corner of your local map: a flower for herbalism, and a shining gold bar for mining. This will let you know which resource you are able to detect . When a resource is detected, a tiny gold circle will appear on the local map. You can mouse over that circle to find out exactly what kind of resource it is. Go to the circle, so that the arrow indicating your character is directly on top of the gold circle. There should be a resource around you somewhere. The color of the resource name will tell you what your skill is in relation to the resource. Red means you probably won't be able to mine it (but if you click it, it will tell you what your skill needs to be for that resource.) Yellow and orange mean you will can harvest it, and get a skill up. Green means you can harvest it and *might* get a skill up. Grey means you can harvest it but will not get a skill up. These are the same colors used in regular crafting, and they mean the same thing in regards to ability and skill ups. If a recipe in cooking is orange, for example, it means you will get a skill up. But if a recipe is gray, you won't.
To mine, simply right click the bright mining icon that appears over the mining point. To gather herbs, right click the bunch of flowers that lights up when over an herbalism point. The icons will be grayed out if you are not close enough, but will light up when you are able to harvest. A timer will appear. When the timer is done, a loot box will appear with the items you were able to find. Right click on the items, like loot, to put them in your inventory.
A mining point will let you mine between 2-4 times at the low levels, and you will usually find one copper ore and maybe a rock each time. An herbalism point will only let you harvest once, but you can find up to three of your herbs, plus one or two additional herbs, when you harvest that single time. Each time you mine, you can get a skill up, same as each time you gather herbs. This means you could potentially gain mining skills faster than herbalism, but there are many more herbs available to harvest than there are mining points. Additionally, there are higher level herbs in most zones than mining in those same zones. Copper is pretty standard until you get past 30, with tin, silver, and iron only occasionally seen (and more miners will be trying to harvest the metals than herbalists gathering flowers!)
To smelt, you need to be near a forge. You will know you are close enough to a forge when your Smelting icon lights up on your hotbar. You can smelt all your bars at once, and you will get the skill up credit, depending on the level, for each bar. For example, smelting copper if it's grayed out will not get you any points whether you do one or 201. Smelting green, yellow, or orange bars will get you additional mining skill ups.
To cook, make sure you're near a fire. If you're not, you can create one using that "Build Fire" command, assuming you have flint and tinder, and a supply of wood. Once you're near a fire, click your cooking icon to open up your menu. Select the recipe you want to make, and click how many you want to make: one, all, or use the arrows to select how many. A timer will appear for each item. If you hit "make all", you WILL get skill up credit for each one you create.
To fish, have your rod equipped, and hit the icon. You will cast your line, and a timer will appear. Put your mouse on the bobber that's now in the water. It will light up. When the bobber splashes down into the water, it means a fish has been hooked! Right click on the bobber to collect your catch. Keep an eye on your bobber, because there are not other auditory clues as to when a fish has been hooked, and if you wait to long, the fish will get away. Make sure to equip your regular weapon when you're done!
If you fish AND cook, check all the fishermen to see if they will sell you a recipe for the fish you can catch. Cooking your own fish is a great way to level up your cooking!
First Aid is the same as cooking, with different recipes, and you don't need to be near anything to do it.
Ah, you found a bug, how clever of you! Let me see if I can divine what went wrong. Let's see...when the timer finished, nothing happened except a message that said "You can't do that right now" or some such, right? And you're stuck in a crouch, skidding along? Well, you'll never be able to finish harvesting that one, so you have two choices: log out, or go harvest something else. Once you successfully harvest again, you'll be out of your crouch.
Or maybe you simply can't harvest the thing at all? That one's a bug, too. It may even be directly related to the previously mentioned bug, where someone else has tried to harvest a bugged spot, so now you can't get it. OR, someone has harvested a spot, but the graphic doesn't fade, so you can't so much as get a harvesting icon over it.
Either way, move along, and try somewhere else. You can send a /bug report if you feel like it, but Blizzard probably knows about it by now. So don't just stand there arguing about it, go someplace else!