What is the difference between the low pass filter and the subsonic filter on an amp? How would a person go about setting these...which one to set first etc?

The subsonic filter is a highpass filter you use to cut out the unaudible/below tuning frequencies to protect your sub.

If your running a ported box, set it around the tuning frequency. Sealed, below 20 hz is fine, but not as necessary.

Just think of it as something that blocks the stuff you cant hear anyways to make life easier on your subwoofer.

Right on, thanks 13.