installation of portable ac unit in garage with a gas water heater
You definitely want a CO alarm anywhere there are people.  

It is best to keep them away from appliances that can trigger false alarms.

Yes, you will get negative pressure while running the A/C, but probably not much, yet it could pull exhaust from the water heater into the room.  

Portable AC units offer lots of ways to run out their vents.  I'd suggest the best workaround is to place the AC unit across the room from the water heater, with yourself and the CO alarm in the middle.

Above all, think safety first.