I run the neck pickup into one channel and the bridge pickup into the other so that I can EQ the pickups separately; then mono out to the SF-2.
Also, and you may already know this, the bass, mid, and treble controls interact with each other. If you turn the treble control, you are moving that part of the curve to which both the mid and treble controls contribute. If you move the bass control you are moving that part of the curve to which the bass and mid controls contribute. I have found it helpful to have a mental picture in my head of how adjusting one control changes the shape of the curve. And of course the shape of the curve is initially formed at the instrument itself, the tone controls, etc. So the interacting controls on the F-2B then move that shape around further.