The Arena is a completely different and separate Battleground system. AV/AB/WSG will stay there just as they are, the only difference is that you no longer need high rank and reputation to get the rewards from the vendors. You spend your honor points and battleground tokens as "gold" so to speak.
The Arena is a new 2v2/3v3/5v5 Battleground area that will be fully implemented after the expansion pack comes out. You can use it now and play practice games called 'skirmishes' but once you reach lvl 70 you will be able to form a team and be ranked which will enable you to earn Arena points which can be spent on great gear.
The main World of Warcraft site is back up and right on the front page will be answers to all other questions you may have. :)