I finally got my mod's installed. I put the JSGME.exe in the main SH4 directory or file thingy and installed it. Then I unzipped my mod's that were in the downloads file. Instead of copy & paste I clicked on the "import mods" that is in JSGME. I just moved them over to activate them and had no conflict's. I'm a happy camper now.

I thought I'd post in case it might help somebody in the future, hope that's ok. Thanks again for all the warm welcomes.