Car Stereo Problems with Amp

hello, i've had a new cd player in my car for a while... and the only way my amp turns on for my subs are if i have the radio on... for a while it didn't really matter because i had an FM transmitter for my iPod.. however i lost it.. i have an auxillary unit for my iPod too, but my amp doesn't turn on if i play my iPod through that.. and the same thing happens with the cd.. anybody know why this would be happening..

-lou

what kind of cd player do you have installed, and how do you have it wired?