you have both your subs and your speakers amped or just the subs?
If its just the subs, then double check your wiring. It sounds like a wiring issue if this started immediatly after installing the deck. Did you use a splice harness, or did you hardwire it? make sure you dont have the POS and NEG switched on the speaker. It will cause the speakers not to play. I know this because I had to fix it for an installer when I had to get some speakers swapped out in a hurry.