Is it okay if i simply Y-off the rear outputs and use them for the amp and the rear spks? Or i could use the Y cable for the front outputs and drive all 4 factory speakers with them and use the rear outputs excusively for the amp.

Yes, both of these things will work. Your choice is: Do you want the fader to control the front/rear balance of the regular speakers, or do you want the fader to control the subwoofer level? I recently switched from the former to the latter, and it works OK for me.

Note that some amplifiers come with a "pass through" output, allowing you to do this without a Y cable.

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Tony Fabris