file management problems

Hi - I noticed 2 subfolders on my HD are missing from Cap 1. I synchronized & they're still missing and another group of subfolders appear twice...it's a mess. I don't know what to do to keep this straight. I just want a simple mirror of the file structure on my HD - just one catalog, no sessions. I thought that if I synch either before or after each time I work on cap 1 that should keep it accurate. Is this a problem for others? Thanks for any suggestions.

ps - I'm trying to import a new catalog from scratch but can't figure out where to import to.
Current location and inside folder don't work, so I select the name of a new catalog I just created & I keep getting the filtering images box that goes on for an hour but nothing seems to happen.