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My workflow for this type of Project is to Import the VOB's into the Project, and place them onto the Timeline. I do a rough edit, by using the Razor/Scissors Tool to cut each VOB (they are now extracted MPEG-2 files, and are no longer in the VOB container, after Import), Ripple Deleting (Delete and close gap), as I go. When I have pared down the material, I then go about Trimming the resulting material, until I am happy with the edit.
PS - Being new to PrE, this ARTICLE has some very useful learning resources.
Once I do this, I have a pretty unwieldy timeline. Is there a way to remove these clips, and save them? I'd like to be able to take them out, or use 2 different versions of them and maybe re-use them in another project.
Well yes, but with one major consideration - the format that you Export/Share to.
The VOB contains already heavily-compressed MPEG-2 files.
If you are going to be editing those Exported/Shared Clips, you can limit the Export/Share via the WAB (Work Area Bar), but I would choose DV-AVI as the format/CODEC. Then, just start a new DV-AVI Project, and Import those DV-AVI's into it, for additional editing.
MPEG-2, from the VOB's, is not the ideal editing format, especially if one is going back out to DVD, as that will entail an additional MPEG-2 compression, diminishing quality, one more time.
Good luck, and this ARTICLE goes into more detail on the WAB.