I mean can you still go into your computer and go to data files to access all of the data? I ask because I can never find any program files from games I install with steam, unless they go to a different place...

There are some threads in Skyrim Mods that explain this.

http://www.gamesas.com/forum/183-skyrim-mods/

Basically it is Steam Apps/Skyrim/Data that contains all your mods and associated files.