I'm a little confused by your question. Are you talking about the air conditioning fans running and the engine overheating? The air conditioning deals only with the inside of the car, not the engine. The engine has its own cooling system (fan, radiator, etc.). Running the AC actually puts more strain on the engine, since the AC compressor gets its power from the engine.
When was the last time you had your engine coolant flushed? Chances are wherever you live must be pretty hot, and it's the heart of the summer right now. My Focus is recommended to have its coolant system flushed every 60k miles.