Congrats!
Here is how I run it; but it's not the only way to do it. There are two outputs on the power supply. Run a cable from one output to the first channel of the F-2B, and run a cable from the other output to the second channel of the F-2B. Now, one set of bass, mid, and treble controls can be used to EQ the neck pickup, and the other channel can EQ the bridge pickup. If you want, you can then come out of the F-2B in mono to continue to the rest of your signal chain (effects, power amp, etc.) of you can come out in stereo maintaining the separation of the neck and treble pickups. My rig is set up to come out of the F-2B in mono.