i've got a 05 lancer that i installed a amp and sub and they both worked fine. now i just installed an aftermarket stereo and my amp and sub only work sometimes. The car can be turned off and the sub will still make noise. when the stereo is on the sub and amp will only work when i have the usb port plugged in it does not work for the radio or for any cds i play. i've got the remote wire all plugged in correctly. if anyone can help it would be greatly appriciated.

 

By "aftermarket stereo" do you mean a deck? If so, the deck probably doesn't have sub-output. Which prevents you from adjusting your system properly, and usually results in it not putting out the best sound.
Also some decks don't match the cars radio cable.. you may need an adapter to play the radio through the system. These are cheap and can be bought anywhere.
But honestly, I don't know much about stereos. These are just some of the problems I have had with mine. I do recommend getting it installed by someone who really knows what they are doing. It's pretty easy to mess something up, which results in the system not running properly.