I typically use my right thumb (I'm generally right-handed when it comes to camera, though I can be ambidextrous at other activities. I think most SLRs favor the right-handed.) for two activies on my D4: Activating (or locking) AF, and changing the starting autofocus point with the sub-selector.
Here's a trick it took me a while to master: If you rest the ball of your thumb on the center of the sub-selector, you can spin the selection point around without ever taking yout thumb off the sub-selector. If you don't stab at a point, but activate it in a direction, you can move the target point in a line.
It helped me to not think of the sub-selector as a bunch of single-contact switches, but as a continual trackpad sort of thing. The only problem is getting your brain around WHERE the new point will be relative to where yout thumb is dragging and where the point was when you started.
I don't use the main selector when taking pictures, only when editing or chimping.