As has already been stated, you use just one copy of SH3 to do a vanilla install, then use the successor to Multi-SH3, which is here:
http://www.subsim.com/radioroom/down...o=file&id=4441
You make a copy of the folder that your vanilla SH3 is in and make copies of it, naming them according to something like SH3-GWX, SH3-NYGM, etc, then use copies of JSGME in each folder to customize that copy. It's all in the manuals.