Launch FOMM and choose the "package manager" option.
Ensure that FOMM and FOSE (Fallout Script Extender) are up-to-date and properly installed.
Download FWE and save it to your harddrive.
Please follow the install instructions carefully: Following this method will make FWE much easier to uninstall as well. It is HIGHLY recommended that you use the Fallout Mod Manager's "Package Manager" feature to install FWE. Fallout Wanderers Edition is distributed as a "FOMOD-ready" install package, allowing you to make your own FOMOD or manually install the file.