my solution: i make 2 saves and i have an excel file wich contains each JSGME mod profiles and their corespondent savegames. sometimes if you try to load a save game after you modify game (adding or disabling mods, etc) will not correspond and you'll have errors, but if you keep some order and make 2 or 3 saves you increase chance to have 1 to work
and keeping a little evidence of modes and saves you don't need multiple installations so you will make disk economy
i hope will help some of you, is very frustrating to loose a good campaign