I don't understand why the subs are cutting out unless there is something built into the deck to prevent you from accidentaly hooking your highs to them and blowing somethimg. You said you had whine in the 6X9's and subs, so I'd rule out bad speakers. If both amps are doing it, I'd rule out bad amps ar f'd up channels. 9 times out of 10 it's a ground issue. How long is your ground wire. The shorter the better. Are you running a ground distrabution block? I would recomend this for multiple amps ao your main ground can remain shor and be distributed from there.
