On my Alpine 9885, it really has no L/P crossover. It only has a bass center frequency adjustment and it's set at 200hz. Adjusting this setting will go into the sub as well as all other speakers. I dunno why Alpine did that with some of there newer models. No real L/P crossver on the deck...

So the center frequency is at 200hz and the amp's L/P is at 85hz right now. So I'm not really understanding what is getting into my ported sub right now, would it be inbetween 200hz and 85hz? Or would it get bypassed somehow

 

Yes, it has a lpf for RCA's, SUB OUTPUT ONLY. That will have no effect on your front or rear speakers.
It also has a HPF for FRONT & REAR speakers only. That will have no effect on the Sub output. From reading your manual, it looks like that works on RCA's and Deck power, both.

These filter's have nothing to do with Bass/Treble eq settings. If your subs are cut off at 85 Hz, obviously, your 200 Hz bass controll won't effect your subs very much.

You've been complaining about this deck for 2 months now, why not just sell it, trade it in or give it away and get a deck you like with all the features you want?

And read your manual.

 

it wont be between 200 and 85. Your amp stops anything higher than 85 from getting to your sub, so the 200 means nothing really.