It is most likely a ground issue. if you use quality shielded RCA's you wouldnt get interference even if the power wire was on the same side. It is however a good idea to run them on opposite sides just in case. crossing them is fine but try to do it at a 90 degree angle. What kind of head unit do you have? That could also play into the issue. If you dont mind posting a pic of your ground that would help.
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