What do you use for combining audio and video? Do you have a Mac by any chance?
I use PS Elements and Vegas Movie Studio 11 (on Win7 platform). I just extract and export the "original" audio track from the video, then sync it with the external audio track using a multitrack audio editor (Audacity or Cubase in my case). It's quite easy actually: first I position both waveforms roughly and then "fine tune" by nudging until they are exactly in sync with each other. Then I trim the external track to same length than the original clip and, after necessary enhancements (eq, amplify etc.), I import the new audio track back to the video project.
I should mention that I rarely bother to record external audio for everyday video clips - I use it mainly for the occasions I record a live gig or something similar. Might be a bit tedious to process, say, hundreds of clips this way.
However, there are more sophisticated, automatic solutions commercially available for both Win and OSX. I remember reading (on this forum?) about such a plugin for Final Cut Pro, can't remember the name though.