I rarely use the main volume knob...I leave it set to about 3 o'clock (this provides a reasonable level generally for my mixer) and always adjust the <PRGM VOL> for listening level. This way I'm never surprised by 'hot' patches...they are all within a reasonable range.
I tried that too beforehand, but it didn't seem to prevent volume differences between patches. But it doesn't matter now that I added the foot pedal.
Btw, the Boss pedal works very well with the OB-6. Plugging in through the TRS volume jack with a stereo cable, it allows you to decrease the volume yet let the effects still ring out a bit, giving a nice after effect. The other way to use it is between the output jacks of the OB-6 and your amp/mixer. This of course stops all sound.
I haven't tried using in the Filter jack yet, as I'm always using it for volume control.