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I'm not sure exactly how the deck sub output works I have mine turned off on my deck and I just use the amp controls

I got the switch system and what i learned first hand about it is this. Mine is the selectable style like Ed has i believe and what your describing but slightly different in the findings for me.
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Very nice AL, very clean man. Now im going to have to visit you again to get a better look at your work lol. I will wait till its all done though. LOL.

Looks real nice man.