(Note: I do not work for Adventure Pilot. I'm just another user who's taking a stab at trying to help...but I may not be any help at all!)
As a reminder of how the process is supposed to work, when you perform an update, you should be downloading a file from the AP website with the name "iFlyUpdatePackage.zip". You should then transfer this file to the root (topmost) folder on a USB drive (if you didn't download it directly there to begin with). You should then either insert the USB drive into the iFly prior to powerup, or else insert it after the iFly has entered Navigation mode and then choose Menu>Check for Update File.
The iFly will then look for an "iFlyUpdatePackage.zip" file on the USB drive, and if it finds one, it will perform the update, and delete the .zip file when complete.
If you or your browser is unzipping the update file into its multiple component files first, then you are essentially destroying the update package and the iFly will not recognize that an update is available. (I think this isn't actualy your problem, but your note is somewhat vague so I'm just making sure.)
Next thing to check is that update files must be less than 2GB in size. If you're trying to update everything at once, you'll bust that limit. Break up your updates into 2 or 3 chunks and make sure each chunk is less than 2GB.
Finally, I have no idea what you mean by "my travel drive keeps filling up with update files that do not show up in the folders after downloading to the unit". Are you saying that after the iFly deletes the .zip file, the space the .zip file was using isn't freed up from your USB drive? That sounds like a weird USB drive issue, not an iFly issue.
Have you tried using a different USB drive? If you've got an older, smaller drive (like 2GB or so), try giving that a shot. The WindowsCE operating system used by the iFly may have trouble with newer, bigger USB drives.
If none of that helps, you might try posting a little more detail about your problem (what computer / OS / browser (and version) / USB drive brand / model (and size) are you using? What filename(s) are you copying over to your USB drive? How big are the update files? Try again to describe exactly what is happening with your USB drive after an update (re: the files that are there but not there). Etc.)
Finally, remember that you can call AP customer support. Look under the "About Us" link at the top of the page.