First, never mess with the INI files in the root install directory. These are the defaults, and if you hose them, you have to reinstall the game.
Look in My Documents/My Games/Skyrim (or whatever game you want). There are two files in there, Prefs and INI. Prefs covers things like screen resolution, INI are game factors. Not sure what GUI changes what parts of these files, but they can be edited manually.
Two things, the files are not complete until you load the game and exit it. I think you also have to be past the opening cut scene. So, with a new game, wait until you can save it before calling the files complete.