I have a new sony 200 watt deck and all factory speakers and such, my factory gain control works with the Radio on only, when i have a cd in it does not work...is there a reason for this?

Yes, I believe the subwoofer amp is connected to your power antenna.

is there a way i can hook it up to work on my cd player as well?

One question for you.... why do you want this to work with your CD.... the gain for the FM just boosts the signal so its louder in your car, it wouldnt do anything for your CD.

LOL, you must be from the old school where people had the FM signal boosters. He'* got a subwoofer amplifier that turns on when it receives a signal from the radio that it is on.

Start by checking the new radio owner'* manual to see if you can get the antenna control to remain "up" when you have the CD on. Or check to see if there is an alternative output for additional amplifiers which provides 12V+ whenever the radio is on.

Yeah your prolly right , im into old cars also so I cross referance things all the time on accident Sorry