Obviously, you should do what I say at your own risk and I see no reason to defend my responses. For the record though, uninstalling through add/remove programs is the correct way. It runs the UNINSTAL.EXE located in C:\Program Files\Common Files\ATX\2007. You can tell that this is the right way because when you do it, it says ATX/Kleinrock product uninstaller at the top and obviously shows a list of ATX products to uninstall. When you select the product to uninstall and click NEXT, you will see that it says "Uninstalling will remove all program components, but will NOT remove your client data folders."
If you had tested this yourself, you would have realized that you get left with the Backup, Database and Masters folders(leaving you your automatic backups, your entire Database, all of your returns folders and all of your updated forms).
Anyone asking questions here in an unofficial ATX community should, of course, be wary of responses you get. The first and best thing to do would be to actually call in for support and speak to a rep in an official capacity.