Chawk,

The 1st steps to tuning a system is to start with the head-unit's internal EQ settings all flat or off or 0. Once the amp is tuned and set correctly, then some treble and bass can be added/subtracted at the head-unit, but only minor tweaking as your music genres changes. if one finds themselves adding a lot of treble or a lot of bass, then the amp settings need to be revisited. Same holds true with an external EQ. small adjustments are ok, but wholesale adjustments means the tuning is off and can actually damage speakers.

The amps gain setting is really the only amp setting that has a "correct" setting. You need to be spot on the pre-clip point or below. below is ok, but past the point of clipping means poor sound went volume is cranked.

The cross-over filter needs to be set according to the speaker type: Subs = low-pass and full-range and HLCDs = hi-pass.

For a 6.5" coax on a tower, 100-120 Hz is a good place to start. The x-over frequency is somewhat flexible and can be adjusted to ones liking, with in a reasonable range. The size, type and application of the speaker is going to dictate the neighborhood of that setting.

The 11 oclock gain setting I gave above is just for a reference, and is no way 100% accurate. But based on the amp, speakers and head-unit, I think its a safe point. if the OP's amp dial is well beyond that point, I would expect him to get the distortion he is experiencing. If the gain is well below that 11 oclock position, then output is being left on the table.