Sololock

i purchased a LS400 that came wired up with 2 10" subs w/ amp
Sounded good but i got the alt, whine and the front right speakers would cut out.
did some investigating:
they spliced the speaker wires from the harness near the head unit to the rear aftermarket amp. (speakers a powered from amp) this sounded good but only the front 2 were working and wires everywhere.
i took it all apart and wired the speakers to the deck. (normal way)

now all my speakers work and dont cut out.

question is. to get my aftermarket sub to work. would i need to
bypass the factory amp? and just wire the how you would normally?