Kevin:
The following is offered with the caveat that I am still tweaking and learning.
First, the question is where to place the SF-2 in your system. You have two choices: between guitar and amp or in the effects loop between pre-amp and power amp. If used between the guitar and amp, the SF-2 acts as a pre-amp, factory set at a 10db boost. You can change this internally to either 0 or 20 db. I can't offer much advise on such a set up as I use mine in the effects loop of my Boogie Mark III.
Assuming you will be using the SF-2 in mono mode, think of it as a 3 channel mixer. One channel is the direct signal. The other two channels are each through a filter. I set one as a low pass filter and the other as a high pass filter. I turn down the gain on both to 0, then tweak my guitar through the non-filter channel. When I'm happy with the basic sound, I turn the direct channel to 0 and turn up the gain on one of the filter channels, tweak it, turn back to 0, turn up gain on the other filter, tweak it, turn it back to 0, and then turn the non-filter channel gain to 10 and start bringing up the two filtered channels, one at a time.
I set the high pass filter channel to accentuate the highs and the low pass channel to accentuate the lows. While I'm still experimenting (as regular readers of this sire are aware, my bass player has appropriated my SF-2 for extended periods while his made two visits to Alembic General Hospital), I have at least figured out that setting one channel at a time by itself seems to work better than trying to tweak everything at the same time.
Good luck with your SF-2, I'm sure you will very quickly fall in love with it.
Bill, tgo