Every system is different, but from what you posted you have a 20hz hole between 80-100. Set the HPF for fronts and LPF for sub at the same point, or put a bit of overlap.
I set everything where it sounds best to me at my normal everyday listening level. If I want to crank it up with the top off I usually don't do anything, but occasionally I'll adjust the bass settings on the HU to get it sounding better.
IMO it doesn't matter if you use the HU settings or amp pots to get frequencies set, but on my system I used both
For the amp gain settings....
-turn all gain pots down to 0
-turn on HU with volume at 75%
-turn up one gain until you start to hear distortion, mark where it is then turn it back to 0
-repeat with all channels (if your equipment is matched well they should be at similar levels)
-turn radio down, set all gains to marked points
-turn radio up to 50ish%, fine tune by ear to blend channel gains together (don't be afraid to experiment with 'bass boost' or whatever your HU calls the sub settings)