It's useful to have the full range of volume available on your pickups - I don't think you should have to reduce vol on guitar just to get a useable tone - reserve this trick for if you e.g. want to clean up a sound for a quieter portion of the song without changing profile.
Apart from adjusting input clean and dist sens as mentioned, try a pure booster in the 1st pedal slot. I usually boost a little, not to the point it sounds like a "boost" as such, but just to get the profile to feel more authentic - i.e. to get the right amount of "bite" and full range of dynamics I'd expect from the amp. However the pure boost also goes into negative values, so if your pickups are too hot, try this - just adjust it till it feels and sounds right - this amount will likely vary slightly from profile to profile, but remain in the same ballpark for a given set of pickups.