When using DualEyes, you end up with a new clip that has the original video footage and the externally recorded high quality audio synced up with the heads and tails clipped perfectly. If you use the Try really hard option, it takes it's time to make the matches. The whole process isn't really long at all. Plural Eyes is a plugin made by the same company. I use dual eyes becuase it makes new clips and you can do it right before importing all of your footage. It works great. I put the link to the trial in the first post.

ExactImage,

That's a great idea and would work but I would like to have the new file names when imported. I know it isn't a big deal, but it would help me organize which footage is the new synced audio clips and which is the original.

     My original clips with scratch audio is labeled MVI_2345.MOV

     My new clips that have been created with DualEyes are labeled MVI_2345_CLEAN.MOV

If I go offline and then reconnect the media, I believe all of the clip names will be the same. I do feed my external audio into the 60D via a cable and the H4N audio recorder, so my original clips audio isn't all that bad. I just don't want it to slip through the cracks instead of having the clean HQ .WAV file synced clips in the timeline. That's where the _CLEAN label would help out if a batch replace footage option with a check box that says "Rename clip names to file names" would be excellent. FCP had something similar to this which worked great. You would right click on a clip and choose rename, then you had the option to rename the file to the clip name or the clip name to the file name. It helped out greatly when trying to keep a huge project organized. If we can add this feature to a new batch replace footage option, that would be AMAZING!

I switched from FCP 7 to Premiere Pro CS6, and what an excellent decision that was. Thank you ADOBE!

- Rob