"What I was thinking was a 1200w two channel for the two subs. An amp just for the tower speakers and the head unit powering the cabin speakers. How complicated is it to switch to the two battery setup?"
Adding a 2nd battery is easy, can be fairly inexpensive, and takes a couple of hours to do. Do a search, probably a dozen threads on this in the past few months.
What are the specs on the subs and tower speakers? This will help you choose the best amp for both (I know you have the 2chnl for the subs already).