Pressing F5 in JSGME usually just refreshes the contents of your available MODS window... some mods actually contain a MODS folder of their own, which usually have some optional mods that can also be used. When you enable the primary mod it writes the contents of its own MODS folder into your game's MODS folder. Refreshing JSGME shows the new stuff that just got added that way.
If this is the case with the mod you're asking about, then it should have a MODS folder with another folder for the Autocannon mod. When you enable the "parent" mod and refresh your view in JSGME you should see the Autocannon mod (whatever it's called) in the available mods list in the left window. If it's there, you just enable it in the usual way as another mod added to your game.
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