Order is only important with "greyed out" mods, that is, mods that have files updated by subsequently installed mods. In these cases you must disable other mod(s) further down the list first to "free" the greyed out mod (as you would have noticed, JSGME adds each newly enabled mod to the bottom of the "Activated Mods" list).
For exclusive mods (ie no files modded by other mods), there is no priority order. Regardless of where they appear in the list they are "equal".
From the Help file:
"- You disable mods by clicking on the enabled mod and pressing the "<" button, or clicking and dragging from Activated Mods to Available Mods. If an enabled mod has had files updated by subsequent enabled mods, you will not be allowed to disable the mod until the subsequent mods are disabled."
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