This is probobally a dumb question (I always miss the text I'm looking for), but I do I start the master update mode?
Do I just load FO3MasterUpdate.exe and it does it automatically?
I didn't see any special options after right clicking any mods.
Am I missing something?
If you renamed your exe to FO3MasterUpdate.exe, then all you need to do is start it. It should run through and do it's work automatically.
If you get an --= All Done =-- at the end of the log you are fine and ready to play after closing the program.
If you get an --= Error =-- then you need to read the log closely and resolve whatever is the problem till you get the All Done.
Do not make any changes to your load order (activating/deactivating/moving any modules) between running FO3MasterUpdate and playing the game.
If you do make changes to your load order, run FO3MasterUpdate again.