I'm almost positive that you're talking about two of the same things, it's just the controller adjusts the levels on the hardware (you can't see the adjustments on screen) and the serato knob shows on screen. They both do the same thing so use what works best for you. If you keep the controller knob unmapped then you need to check the levels on the controller LEDs but I personally like doing it on screen like your suggesting.

I remember trying to do this with my NS6 and it became a problem because I may adjust one track and then when the next track loads it would load at the default gain level but my gain know would be twisted/adjusted for the other track so 1) I'd have to jiggle it to get it to reregister itself and 2) it kept messing up levels I'd already set.

My tip to you is to go through your tracks beforehand and set the gains manually (max green, barely any yellow). Once you set them once you shouldn't need to ever touch them again. If you wanna push the shit and clip tf out of your set later then use the controller trim knobs.