My approach is to find a generic Fender tone on the neck PUP.  That usually means rolling the filter back to 1/2 - 1/3 and (depending on whether I want some extra zing) disengaging the Q switch.  I always run the filter on the bridge PUP wide open and engage the Q.  After I have that set, I'm just adjusting the pan control: if I need a lot of bottom I favor the neck, if I want clarity and punch I favor the bridge.  Before I got my Alembics, I NEVER messed with the on-board electronics.  But as you all know, you can really get a nice wide palette of USABLE tones from an Alembic.  I have some patches set-up in my Boss ME-50B for a slap tone and a hollow body tone; but other than that, I do it from the bass.