Re: If the same QVW overwrites the User Documents why can't I point the same location for Source and User Documents?
If you don't have Publisher license - this is all you can do. There is only one location.
If you have Publisher, it doesn't make sense to keep all in one folder. You maybe have QVW files in source which you don't want to show on the access point. Besides, the documents published to the user folder don't have script. So, you can allow user download documents without disclosing your script secrets.