The simple audio recorders in most presentation programs are convenient for recording narration, but I almost always end up wanting more functionality than they deliver.
So unless I’m in a big hurry, I prepare audio separately in a dedicated recorder/editor such as Audacity or Garageband, and then upload it to my presentation. It’s another step, but in the end the process is easier and less frustrating than trying to make-do with the recorder in PowerPoint or Captivate.
I often use a USB mic plugged directly into the computer; sometimes I’ll use a portable digital recorder and then upload the recording to my computer. Either way, I can edit and add EQ, noise reduction, reverb, and other effects and filters to clean up the track before I apply it to my presentation or e-learning session.