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I saw an entry in the FAQ that referred to grounding the aux in RCA sleeves, but I'm unsure why this would be necessary?
Because it might help get rid of a ground loop.
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If so, what's the best way to go about grounding them?
Attach a ground wire to them. If necessary, buy the appropriate male and female connectors at radio shack and fashion an adapter with a ground wire coming out of it.
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apart from some alternator whine, but that's due to a non-optimal amp grounding which I'm going to fix ASAP
You must also fix that if you want your aux input to work properly.