I'm not to worried, i have multi installs of Skyrim so i can add mods to this sucker to hell and back if i need too. Setup a new User Account in Windows name it Skyrim or whatever make it as acc administrator, log in to that acc and install Skyrim. Make an acc for each install & use the Steam fix for each install to take steam out of the picture for good, so multi installs are not a issue. And i grab all Skyrim updates of the internet without steam.
I have 1 heavy modded install, 1 clean install untouched, and one lightly modded install.