Chris, personally I tend to use pencils when the water conditions dictate, and that drives it rather than the type of terrain. Anytime there is chop in the water, then I tend to reach for a long, skipping type pencil.
The other time would be when there are lots of fleeing Long Toms around. I find it hard to get the lure to work properly in calm water though.
As for technique - nothing very clever. Stick the rod in your belt with quite a high angle and use a steady retrieve (does not need to be too fast) with a gentle up-twitch. The speed of retrieve and the twitch need to be just enough to get the lure skipping authentically.
With lures which are dual purpose popping pencil types (eg SS Trumpet, Heru Skipjack), then you can mix up the skipping retrieve with some gentle pops as well.
One other note - in my experience and that of others I have spoken to, the speed and ferocity of a GT taking a pencil is incredibly spectacular. Really fast and aggressive.