One thing you do not want to do is punch down at a shorter opponent; that doesn't keep him at the end of your reach, it shortens your reach and gives him opportunity to punch over the top. If you watch Bob Foster in the video, you'll see how he does a bit of both things mentioned. He lowers himself by widening his stance, and he jabs from where you should be jabbing from, about chest level.

For some inane reason, the trend in today's version of boxing his too hold your hands far too high. Your lead hand should be chest level to keep it out of the way so you can counter with it. Your rear hand should be responsible for 80% of your defensive work and your lead shoulder should take up the bulk of the rest.