Some kits work with A/C, some do not. It is more a question of the downpipe clearing the compressor than anything else (like IC piping getting in the way of the condenser coil).
If you are building a custom kit, you just need to know if the manifold will allow you enough room to clear the compressor. You kind of want a little distance, as 1500*F exhaust gas has a way of messing up your A/C.
I live in Florida and I deal without A/C. Go a week without it and you'd be surprised.