It would be easyest to let JSGME create the mod folder. Make sure you JSGME is either in the gamedir, or the shortcut is set to start in your gamedir.
http://www.subsim.com/radioroom/showthread.php?t=192374 contains all the info you need .. altho tailored for a specific list, the info is more or less universal.
You extract the mod dir to your mod folder. Make sure that the structure is:
\gamedir\MODS\modname\data not \gamedir\MODS\modname\modname\data