I'm obviously a HUGE fan of the 408 system, and I have a few favourite settings that I use a lot. Here are my top ones:

Bridge singlecoil, tone on 10, volume on 9

Great for cleaner parts, with or without chorus, for apeggios and acoustic flatpicking style stuff

Both pickups, neck humbucker and bridge singlecoil, tone on 8, volume on 7

The "Keef" setting, great for crunchy rhythm parts.

Neck humbucker, tone on 7, volume on 10

A great warm soloing tone without the flabby/muddiness of traditional neck humbuckers, nor too much snap from a singlecoil. Add a good amount of gain and the tubular woody tone just sings out.

How are you getting the tones you want - I'd be interesting in trying your settings myself!