Our first year was pretty hectic and as such our CAD files were splintered across the Windchill server. Half of the kids did a decent job getting them into the "CAD Models" folder, the other half would wind up with them on the main Windchill page as they would forget to update the file path when checking in the parts. AT the end of the season, I moved all of the first year's files into a 2015 Recycle Rush folder within CAD Models.
The kids still forget to update the folder path when checking in from time to time, though, so I check the Windchill page every few nights and cut/paste accordingly and attempt to train the kid into maintaining a good folder structure.
To move parts, it's fairly easy. You only need to check the box in the Windchill folder structure next to the part you want to move and click the scissors/cut button.
Then you need to navigate to the folder you want it in and click the paste button.
In that regard, it's the same as working in Windows Explorer except you have to use the cut/paste buttons instead of having ctrl+X / ctrl+V capability.
Hope this helps. Let me know if you need more detail.