if you play single missions is not a problem if campaign files are modified, but if you play campaign you must be careful and don't forget to make backups of files you're modding
they are here few tutorials about adding ships in campaign i'll put the links for you
or you can use "save task" option in JSGME to save modification list for each ship, or multi sh4 to run more than one instance of the game
http://www.subsim.com/radioroom/showthread.php?t=190455