Erm, well off the top of my head..... and assuming the both amps are 2 channel.....and your HU has pre-out and sub pre-out....
Run main power cable from battery back into boot (fused of course)
Run rcas and switching line from head unit to boot
wire in both amps to power and take a line from the switch line to both (in order to signal to both amps to turn on when HU is on)
Wire from amps to subs and 6x9s (setting freq. cut-offs on either the amps or hu - if necessary)
Nothing much to it really, theres more to the boot build side of things than the wiring side, its the simple bit.