If it's a bass knob that ties into the amp it's basically adjusting gains on the fly. I'll assume you're talking about something like the PAC LC-1, which basically attenuates the RCA signal from the HU to the amp. When such a knob is all the way up it's getting roughly 100% of the signal, as if the knob weren't there. It can only reduce the signal, it can't boost it.
I have three such knobs (for the front, rear, and subs). I can adjust these values from the HU, but I like the simplicity of three physical knobs.
Set your gains with whatever settings you adjust normally at their highest setting. I don't listen to my music with a flat EQ, I go through my HU's presets (which have settings for bass/mids/treble on a scale of -8 to +8). I often use the "Powerful" EQ setting for Hip-hop/trap/dubstep, etc. which goes something like (+8 bass, +3 mids, +2 treble). There's another setting (Top 40 or Pop - something like that), that I don't use as often that has the treble at +8. I think the highest any of the presets goes to for mids is +6. So, when setting the gains I put the bass to +8, mids to +6, treble to +8.
I have bass boost off and my subwoofer set to 0 (on a scale of -15 to +15). I never turn up the subwoofer setting here. I then turn the volume up all the way (many people suggest 3/4th of max to prevent HU clipping, this is a good idea, just be sure not to stray beyond that, you'll still get max power). I use a -5dB test tones (from a test tone generator app) and an oscilloscope.
The reason I turn everything up before setting gains is that way I can do that way I can have those settings when listening to music and know it shouldn't be clipping. If you set your gains with a flat EQ and then use the EQ to boost certain bands you'll easily enter clipping territory.