So my 4 cylinder vtec honda started overheating and i quickly realized I was pretty low on coolant. I filled it up and it started idling rough and had trouble starting after running a while. I am fairly certain I got air in my coolant system and need to bleed it and hoping that will fix it. But I also noticed my radiator fan is not working which i think is why I how i lost coolant in the first place caused by evaporation and old radiator cap which i will replace. I know the fan motors are good and relay is good. I shorted out the cooling fan switch and fans will turn on when engine is off(keys not even in ingnition), when i turn the car on or start engine the fan turns off. This strange issue has me stumped and any insight would be greatly appreciated.

 

Sounds like you are testing the wrong fan switch....one controls the fans when the key is on. Another controls the fan when the key is off.

Sounds like you have a cooling leak, fill the system and get the air out. Then rent a cooling system pressure tester and check for leaks....many of those testers will also test the cap.