Directly from the download page
I prefer to use the Masterupdate file from http://www.fallout3nexus.com/downloads/file.php?id=1925 download page since it is the updated version. It has the FO3Edit, FO3Masterrestore, and the FO3MasterUpdate files so it is less work.
==========[Known Issues]==========
-If you are having problems crashing with the MiniHideout please see the following mod: FO3Edit by ElminsterEU
http://www.fallout3nexus.com/downloads/file.php?id=637
This fixes Megaton, random, load or save crashes most of the time...
Steps for use:
1. Download FO3Edit
2. Copy the FO3Edit.exe to desktop
3. Rename to FO3MasterUpdate
4. Open up FOMM (Fallout Mod Manager) and check the mod
5. Click the FO3MasterUpdate.exe with FOMM still open (then close window when it says it's finished)
6. Launch Fallout 3 through FOMM.
You do not need to install the esp that comes with FO3Edit. And you will need to do this each time you install a new mod.