First, place the Unreal File Organizer application and the UFO Files folder in the same folder with the Unreal application as shown below.
 
Now, whenever you want to add a new map/mod package to UFO's list of managed files, just drop the folder into the "UFO Files" folder or, if UFO is running, drop the folder on the package list and the folder will be moved or copied into the UFO Files folder for you. Each folder within the "UFO Files" folder should contain a single map or mod package (ie. a batch of related files that should be installed at the same time).
To install a package, launch UFO, highlight the name of the package that you want to install, and click on the "Install" button (or just double-click on the name). UFO will place all of the files in their correct Unreal subfolders and beep when it is done. If a file already exists, UFO will not install the new file and will warn you of the problem.
To remove the package, launch UFO again and click on the "Remove" button (or double-click the name again) to reverse the process and return the files to their proper folders.
UFO will not allow you to delete a package folder that is currently installed, but it is possible to do this manually. (If you later decide that you no longer want to use the installed files, you will need to remove them manually in this case.)