Theres at least three different locations that have Skyrim folders, that contain the .ini files for the graphics settings, the default, etc. and the Data folder with the esm files and such inside it. But only one of them actually does anything. And it doesnt seem to be the same one each time. Sometimes I have to use the one in theProgram Files folder. Other times I have to use the one in the Steam folder, and sometimes I have to use the one in my c:\users\mousemage\Documents\My Games folder.

I'd really like to know exactly which of these folders actually controls which aspect of the game, because duplicating every file between them is tedious.

The changes you make should be either the Skyrim.ini or the Skyrimprefs.ini file in the My Games folder. These files shouldn't be located in the data folder. There may be mod ini files located there that you can edit.

What ini files are you trying to edit specifically?

There are exceptions such as if you are using Mod Organizer (MO). You need to edit the ini files from MO not manually.