For what it's worth, I have found the Presence control to be a big key in achieving a subtle smooth drive with both single coils and humbuckers.  Since it controls the negative feedback circuit it can impart some drive and harmonic distortion to the clean channel. 

In the clean channel with the PAB off, adjust the tonestack to your preference.  Now use the Volume (far left) and the Presence control to get some added harmonic content and even some bite to the cleans.  Turning the Presence control clockwise decreases the amount of negative feedback added back in to the circuit and in so doing increases harmonic distortion.  Some of my favorite clean tones from Danny Gatton and Roy Buchanan to Stevie and Jimi aren't really all that clean if you listen carefully.

Now go to the Overdrive channel and adjust.  Switching between the two channels set up like this has helped me achieve some great tones that had always eluded me with other amps.  Some nice singing sustain to the cleans and some great greasy blues and rock tones.

Also, don't overlook the usefulness of the Jazz switch even if you play Blues or Rock.  This function will change your settings a bit to get your main sound (compared to the Rock function) but you may find it helps even things out when you bypass the tonestack with the PreAmp Boost.