You really need to get with a local hvac contractor that can design a system that will work for you. The best one is the Honeywell IAQ system. Being that you have two different heating systems, again a HVAC contractor can figure out the best option.
You can control with two thermostats the different heating systems, but again as I stated, it is the A/C that is the problem. Sign up over at diychatroom.com and the hvac contractors can tell you the best way to do this, so that this conversation is outside of this forum.