The Rollback button undoes any changes Commander has made to your game files when loading the game from the Commander interface. You should always "roll back Commander" before making any other changes to those files, either with manual edits or by enabling/disabling mods in JSGME.
There is also an option in Commander for auto-rollback, which is what I described above - if selected, the rollback will be performed automatically each time you exit the game. That means if you decide to do some modding in between sessions, you don't have to worry about remembering to open Commander and telling it to roll everything back (by clicking the Rollback button).
I recommend selecting the auto-rollback option, it's just easier and safer.
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