Why can't you just make your entire #UP# folder into a jsgme and call it jsgme_WWII in the jsgme window, make another one from your #UP# folder you made for Ultra_Spain and Call it SCW_1936 in your jsgme window. Each of those files would have the #UP# folder in it. You can disable one of them and it goes away, and then enable the other, just remove the #UP# folder that remains in your install so when you enable WWII, or SCW there are not two #UP# folders in your root folder, it should work just fine.
It does on my computer......
jsgme Folder/
#UP3_WWII/
#UP3#............ this will have your UP mod folder contents for your standard game that you saved to your documents folder in case you hose it up...
jsgme Folder/
#UP3_SCW_1936/
#UP3#...... this will contain your Ultra_Spain package and any other mods you want to add, I removed the effects package and inserted Gurners, Ecranwide, sound mod
of your choice that works...... just remember to give it time to completely load before you close it.
Cheers
Hoss