All files are compressed from, and should be extracted to, the maps subdirectory. They should work out of the box with the most recent svn version of Bos Wars (at time of writing, end of Jan 2008) and release version 2.4.1, or pre2.5. Note that if you wish to play against someone else, both parties must have a copy of the relevant map - the game, so far, does not copy it from server to client (although this is planned for a later release).
The large file sizes are mostly caused by the large png imagemaps. They don't compress very well.