For Jerry tones... treble 10, mids 5, bass 1 to off. The tone controls are really nice sounding in any position. For a Metheny-esque jazz tone, treble 6-7, mids 6-7, bass 3 works. All 3 set to noon sound good. I haven't found any position that doesn't sound good.
This is Brad's explanation of the output pad knob. I keep mine around 10-11 o'clock.
"Right next to the output jack on the rear of the preamp is the "pad" knob. By the nature of this preamp circuit, the output level can be extremely hot. This knob helps to pad down the output signal level to be more usable in most situations. Initially try your preamp with the front panel "Gain" knob set around noon to 1 o'clock. Then use the rear "pad" knob to adjust the final output level to best match your setup. You may find that the pad knob wants to be set down below noon, but feel free to set it wherever it needs to be. This will optimize the "gain structure" as well as minimize noise. "