Why are you separating your alts and running two 12V systems? If you are going to do that, then why not get an adjustable voltage alternator for your secondary alt and run 14V or 16V to that system? Not trying to cause any issues, but that just doesn't make a lot of sense to run two separate 12V systems.
If you just want 12V then I would suggest running both alts to the front battery and then power from front battery to the back. Then you would have both alts to cover the amperage draw from the amps. If you were doing this I would suggest a D3100 in the back if you want to see very little drop.
If you are going to run two separate 12V systems, then I would suggest running a couple D3100 in the back if you want to see little voltage drop.
What I would really suggest is running the stock alt for your 12v and then the secondary alt (being adjustable) running 16V. The AQ2200d is rated at 2500 X 1 at 1ohm running at 16V. You would see a huge increase in power and a very noticeable audible difference. On this set up would suggest 4 of the XP1000 batteries.
Again not trying to say anything bad, but just give you some options that most people would kill to have. It is your system, so make sure and do what is going to make you happy.