There is a difference.
If you edited files that in a vanilla installation were not unpacked, then you can go either way.
If you edited files that in a vanilla installation were already present, you'd be more inclined to use a mod folder.
Either way works really, but that's for simplicity's sake.
What I would recommend you do is this:
Download alpaca's mod folder installer.
Install it, calling your mod "MaliMod" or something like that.
Then move all those files and folders elsewhere first to get an overview.
Now move all the files you modded for your mod into the MaliMod folder to where they belong, overwriting when prompted.
Now zip the whole thing and upload. The person downloading will only have to place the MaliMod folder in their medieval2 folder and run it with the shortcut provided.
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