NOTE: If you are using Windows Vista or Windows 7 it is recommended that you install FO3/FONV and the matching versions of the Geck in a folder other than Program Files or Program Files (x86). These folders are protected by the operating system and require you to take additional steps when creating and using mods. If you have already installed them into one of these folders, either uninstall them and reinstall them into a location like C:\Games or C:\Fallout, or, when using the Geck, always run it as the administrator. See the note below under Loading and Testing Your Plugin for more information.
So this means that if I have Fallout 3 and the GECK in the directory that I'm used to (C:\program files\steam\steamapps\common\fallout 3), mods may not work? If so, should I move my Fallout 3 from there into my "steam/bethesda/fallout 3" folder, along with the GECK?
Although it says "... or, when using the Geck, always run it as the administrator.". I am an administrator, so does this mean doing it in the origonal directory is fine?