Lets break this in to 2 parts
Turn on/off thump is usually created when the amp(s) and main source unit are turned on or off at the same time, like wiring then to the same switch. Rarely will it damage anything, but darned annoying.
I highly suggest relocating the head unit's IGN turn-on from the key switch to the rocker. leave the turning on of the amps, to the head unit.