Best way is to put a looper after the Input1. Record a small section of music similar to what you normally play for that preset.
Now I can't stress this enough, turn the volume on the Axe down quite low.
Add a PEQ after the cab, add a low cut around 80 to 120hz (or do this on the cab block for the selected cab). Best way with low end is remove it slowly, when you hear the sound thin out, add a little back in.
Subtractive EQ
Now turn the Q value on the compressor channel up full, then turn up the gain to full (so you have a peaking spike). Now adjust you Axe volume so you can hear comfortably. Now use the frequency knob to sweep the eq spectrum. If you hear any sounds you dont like such as boxy sound or whistling, use the gain know to reduce that frequency by about 3-6db.
Do this across all the PEQ channels. Then disable the PEQ to see what effect it has had.
Compression.
General rule of thumb is this: if you are going to compress, EQ first as the compressor will exaggerate any annoying frequencies, if you have rumble in the low end, a compressor will make it worse, remove it first.
Additive EQ
Once you have added EQ, then compress, it is sometimes good to add another EQ but this time to not remove frequencies but to add them back in where applicable.
Before you EQ, get the sound the best you can using the Amp EQ, Input and Output EQ and the Cab EQ section. It will make it easier to EQ later.
I hope that helps.
Mike