i was adjusting the subbox in the back of the trunk and when i went to start the car for some reason the subs wouldnt work

i checked all the wiring and they were all connected in, as well as the amp settings, etc. and nothing was out of the ordinary...i turned off and then turned on my car and the subs started to work again but were not hitting as hard as they once were....anyone experience this? or know how to fix it?
also another question- how much of a decrease in quality should i expect if i splice on wires (signal, power, ground) onto the existing ones into the amp so that i can move it to a diff part of the car?