The neutral setting of the amp is tone controls at noon, and filters off. Start there. If you feel like there is too much upper treble, then slowly engage the VLE, which will roll-off more and more of the treble range as you dial it up.
The VPF control is kind of a 'one knob' control that is similar to boosting the bass control, cutting the low mid control and boosting the treble control. IMO, that is best used either not at all, or sparingly, since it extends the low end beyond the frequencies that most cabs can make use of, and the individual tone knobs give you more precise control anyway. However, with some very midrange voiced cabs, it is a useful control up to around the 9 o'clock level.
Regarding gain setting, set the input gain just below the level where the clip light comes on. Really play your open E string hard (turn down the master so you don't hurt your ears) and with your other hand, dial the input gain until you see that light start to flash. Then turn it back a bit. Then, adjust the volume you need with the master.