... .usc files can be either part of regular packages or are placed in Common or Local directory. ...
If I understand the code correctly, "Local directory" means a directory named "UppLocal" and residing in the directory containing the TheIDE program file (commonly ".../upp") which has to be manually created.
I understand it that you can place it in any local (= non default) directory (=package) whereever you create it. As you say C:\upp doesn't make much sense because it is deleted each time you update.
so eg D:\MyApps\myPackage would be a local dir at the "SetMainPackage" Screen just add a new assamly (right click on the left column) and point it to D:\MyApps. They won't be deleted and you can add .usc files to your packages as much as you want.