Warren - I'd leave my tone knobs all at 12:00 and leave them there if I were you. The Valvetronix was meant to model a specific amplifier with each model...all the models have tones that are inherent to their design. Why make it harder? When you get the sound of each amp model in your head then you can adjust to your liking later on. My tone knobs on the Vox are almost always set straight up and they sound wonderful...even on all the models. With my Marshall it's different of course.
Tim - There isn't a set rule of thumb for tones. It's a cliche' to say anymore...but tone is subjective. Depends on who's listening. Straight up tone knobs on your own amp might be an answer for you. Concentrate more on your playing.
Guitars/Bass - MIM Fender Classic 50s Strat, MIM Fender Standard Strat, Squier Classic Vibe 50s Tele, Gibson Les Paul Studio, Epi '56 Gold Top Les Paul, Martin DSR acoustic, Sigma Martin Auditorium electric/acoustic, Squier Jazz Bass.
Amps/Cabinets/Modelers - Model 2558 50 watt Marshall Silver Anniversary Jubilee combo w/ Celestion Vintage 30s, 4x12 Marshall cabinet w/25 watt Greenback Celestions, Fender Blues Junior w/ a couple of Billm mods, Line 6 POD 2.0, Roland Micro Cube
Pedals/Effects - Cry Baby Classic Wah, Boss TU-2, Boss NS-2, Boss RC-2 Loop Station, Ross Compressor, MXR Micro Amp, Danelectro FAB Echo, Danelectro FAB Chorus, Danelectro Chicken Salad, Marshall Guv'nor Plus, Marshall Echohead, Duhvoodooman's Zonkin' Yellow Screamer, Digitech Digiverb, Digitech Bad Monkey, Dunlop Fuzz Face, Homemade Loop Bypass pedal, Duhvoodooman's Sonic Tonic (Maxon SD-9 clone +), Voodoo Labs Superfuzz