Cory, What happened to the RCA wire? Did it melt? Sounds to me like you have a pretty serious ground loop. If I understand correctly you are wiring your head unit to one battery and your amp to another? If this is the case your RCA's might be trying to carry the ground current to balance the batteries. In addition to ignition noise you will likely burn up your RCA's again. The solution would be to wire everything but your deck's turn on lead to the same set of battery. Best case scenario you should pull the yellow and black, power and ground to the deck, off the same source as your amp. If you wish to maintain the existing switching you can probably leave the red wire to the deck where it is now, but not the black.
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