When running, it will automatically check PBW2 for games that are due (all players are uploaded, and/or deadline expired - see PBW2 game setup options)
Follow the ReadMe file for details, but the highlights include:
Make a copy of your SE4/5 installation for safety. Fill out your game host login/password along with the paths to SE and your mods in the INI file. Run Autohost3.exe The known games list will start out empty, and fill in as games come up for processing.