Or do you mean, reconnect the Bose wiring up at teh drivers kick panel.
Then in the boot, instead of having the wires running into the Bose amp, have them running into the new amp?
Yep, that's exactly what I mean.
Ignore the wires in the bose harness that come from the speaker outputs on the head unit (insulate them so that don't short, though).
Run some line-level cables up from the head unit to the (new, non-bose) amp in the boot.
If the new amp has modest current consumption (under 20 amps) you can take the power feed from the Bose loom (thick red wire), or run a new feed.
The speaker outputs of the amp can go back into the Bose loom, up to the driver's footwell where they will then connect with the existing wiring in the car loom.
You can also find a switching signal (Read with white stripe, IIRC) in the Bose loom that turns on the amp with the head unit power, although check that this is on the right pin on the ISO connectors at the back of the head unit.
Kevin