Sure thing dude! I basically go about the whole thing by first playing the guitar clean and with a lead tone to see if I'm able to get enough sustain. I play with a medium/higher action string setup so I need the sustain to come from the pickups and their height. Okay so once I find the height of the pickups that offers the best sustain, I'll fine tune for EQ. If the lowend is too mushy or when I rest my palms on the bridge area the strings come too close to touching I'll lower the bass side slightly. I test lowend usually on the Low E and A strings by picking them open first, then fretted somewhere down the neck. For the high E and B strings I determine if they are too bright and if they are I will back them down slightly. You don't want to lower them too much or you'll kill the sustain. This is mainly for humbuckers but single coils can be more tricky. I usually lay the guitar in my lap with the amps fairly loud so I can hear the differences, and just strike the open strings. I just use a screwdriver to adjust while I hit open strings to get the best tone for my ears.
-Justin
'67 and '74 Fender Twin Reverbs, '74 Marshall 1987 lead mkII, Metro Superlead 100. Pedals from TC Electronic, Ibanez, Dunlop, BK Butler, Electro-Harmonix, Fulltone, Maestro/Gibson, Loopmaster switching, VoodooLab, Boss. Gibson and Fender guitars, Dimarzio pickups.