I got an aftermarket deck in '06 for my Evo IX SSL with the Soundgate adapter. My biggest gripe is how the subwoofer is treated like a rear audio speaker to the deck. Is there a fix to this?

 

I doubt it, because the sub probably shares a signal with probably the rear speakers. You definitely wouldn't, at least IMO, be able to control the sub on the factory deck, maybe an aftermarket with dedicated control.