I've only used BAMT with from two to five cards. Never had an issue not recognizing cards. Only once but it was because the motherboard didn't support running cards in all five slots. What motherboard are you using? BAMT works great in my opinion, I've got the rigs down in a corner in my basement so it's nice not always having to go down there to administer them.. Plus I can log in from my iphone or work computer, etc.

I'm also pretty sure that BAMT doesn't come with drivers for the R9 cards, I installed those drivers before I tried using my 280x cards on it.

As for OP, go with two 1200w PSUs or a 1300 + 1000. The psu combination you have may work fine but if all things peak out at the same time you could run into issues. Better to have more and not need it than the other way around