You could make your changes under TempMods, but every time you Refresh Mods Automatically, it'll over-write your progression.
You could also host your progression files on a site somewhere, like pastebin.com, and make a "My Mod" for it. This will allow you to keep up to date, while continueing to use your progression file.
In order to make a My mod, you'll need to know which download links are in the original mod, and copy them into your new My Mod. Your progression.xml link should go last.