DEFINITELY want to bypass / deinstall the amp. Your pioneer (w MOSFET 45/50?) is overdriving the poor front end of the 'premium' amp, causing the distort-o-matic.
Other choice (not worth it) is to get/make some adapters to lower the power of the speaker level outputs to line level, but then you may lose fidelity, so it is not worth it.
Bypass-o-matic.
Rob-o