I had a similar issue last week, a good high pitch whine from my engine coresponding to revs.

I just tightened down all my connetions and the noise hasn't come back.

as for grounding I've got my deck grounded to the frame near the deck, aswell both of my amps are grounded to the frame in the trunk.
aditionally I've got a small ground wire linking the two spots on my frame where I've grounded to (the deck ground spot to the amps ground spot).

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Inside my 96 Nissan Sentra:
Pioneer DEH-P8600MP
Pioneer Premier GM-X924 Amp Powering 2x JBL P632 midbass, w/ CerwinVega Tweeters, on Pioneer passive xovers
Pioneer GM-X922 Amp Powering a Pioneer Premier TS-W1041DVC sealed
Awaiting spring: Pioneer CD-635, Clif Design QX6500C, a 0g run and adding a Sony LS-1065g