id say place a file that only contains paths to other files/directories in the standard location (for example %APPDATA%\fspaths.cfg). then you can configure these paths in the launcher or use defaults (for example my games\fs2). then the actual settings/application/mods directories can be placed anywhere. though id default them to my games\fs2open\settings, program files\games\freespace 2\, and my games\fs2open\mods, respectively. you might want to install the launcher and the fs2open engine in different places, though, id prefer to keep stuff in as few places as possible, for ease of backup.