its really easy, just start with a fresh brand new game install with no mods installed and jsgme already added, then make a copy of the entire sh4 game file found inside the ubisoft one and then rename it something different. do this as many times as you want for as many different copies of the game you want to run. you can put them anywhere you want to but I just keep them all inside the ubisoft folder on my computer and name them based on what they are used for like sh4-RFB or sh4-TMO.
after you have copied them you need to open each folder and copy that games exe shortcut and that games jsgme folder exe to your desktop and then rename both of those to the same name of that game so you now have separate game file and separate jsgme utilities for that game and if you use it do the same for the mission editor as well.
when you save games name the saves accordingly because opening the wrong save file in the wrong game will cause CTD
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