Originally posted by DaiveR:

Try do one simple trick. Worked for me in other games in pc.
Do the full copy of a game. Put it anywhere you want (dont put in steam lib directory).
So. Then just mod the COPIED game. Run it, from its copied exe.
This trick force steam to see, what game are you playing, bcoz its legal-buyed one )
BUT all patches and updates will hit that one that non-modified, in steam lib folder.

Now that I think of it, for the longest time I simply turned off all automatic updates from Steam for Skyrim. Essentially accomplished the same thing.