This article has links to several threads on Camtasia, CamStudio, and also FRAPS. Some of those threads go back to earlier versions of PrPro, but with a bit of interpolation, one should be able to glean a lot of good tips from Jeff Bellune's comments. Though he concentrates on Camtasia footage (with the TechSmith CODEC's), much will apply to working with video screen-cap software. http://forums.adobe.com/thread/453044?tstart=0
Also, a good starting point would be to use one of the FRAPS Clips to "create" a New Sequence for it. After it has been Imported into the Project, just drag one of those Clips to the New Sequence icon at the bottom of the Project Panel, and PrPro will create the Sequence for you, per this image:
Good luck, and hope that there is some help in those links in that article.