If you can't get JSGME working its not really needed, BUT if you decide you want to remove the mods you could have to do a complete uninstall/reinstall.
What i did was create a fresh install, then make a copy of it to a new folder under another name. Then i just drop the mods into the correct folder and allow it to overwrite the stock files in the fresh install.
If i don't like the mod then i grab the files the mod overwrote from the renamed stock version and put them back into my install.
Its more complicated, but its the way i have modded many games over the years and old habits die hard. I have nothing against JSGME, Its a great program but I have always done things a little different.
