I've just started using JSGME after a fresh install and after previously copying and pasting mod files into my Data folder and I can confidently say that JSGME is the absolute mutts as a bit of kit. I have had a few issues where I had placed a mod into the Mods folder and they hadn't worked but on closer inspection the folder layering had been wrong.
As long as the mod that you place into the JSGME mods folder is along the lines of "Mod name/Data/mod files" you should be OK. Also, be aware that some mods will overwrite others when you enable them.
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