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I recently added a sub to my setup, and I'm trying to set up the high and low pass filters on the HU to configure the sound. I am probably confused, or doing it wrong, so I figured I'd ask here.

Whenever I set the HPF to 80hz, it affects the sub as well as the main (un-amped) speakers, which results to little to no bass coming from the sub, or anywhere else for that matter. To get around this, I set the EQ settings off so the main 4 sound a little flat, and cranked the max gain on the sub amp up. It sounds decent, but what I would really like is for the HPF filter to work, so all frequencies above 80 play on the main speakers, and everything else on the sub. This would allow me to turn the sub volume lower and use the EQ to tweak the sound.

Sounds liek you have the RCA's hooked up wrong. You should have the RCAs on the non-fading output, or sub output, whichever your Hu has. It sounds like you have it hooked up to either the front or rear output.

They are on the correct RCAs, because I can control the sub volume directly from the HU.

make sure subwoofer is "on" in the alpine menu.
set HPF to 125Hz, 12dB Q
set LPF to 60Hz or 80Hz, 18dB Q
see how that sounds