on the back of your headunit there is a wire that shouldnt be connected to anything, i beleive its Blue with a white line, connect your remote wire from your amp to that wire on the back of your headunit...this way your amp will know when to turn on
you can run the wire right with your rca's, if your head unit came with a wireing diagram, use that, but it 'should' be blue with a white like, like jeff said. There will be a small delay between turn on of the head unit and turn on of the subs, but that's normal.