There are only 2 files in Mario and Luigi Bowser's Inside Story.
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delete the games .exe file and redownload with the mod inside the main folder. Then delete System32 files to improve ur graphics output
Nintendo ds files
Just extract one of the .rar files into a folder. You don't need to do anything with all the other .rar files.
copying files over a network?
Two ways: 1) Buy or build a ROM interface device, and download the file directly from the cartridge, or 2) perform a search on google.com for the name of the GBA game you wish to download and keywords that imply a download, such as "Super Mario Brothers GBA download" or "Super Mario Brothers GBA ROM". Many sites host these ROM files, plus many Torrent sites will have downloads for these files. Be sure you actually own a copy of the game, or you risk legal issues (you do anyways, since piracy is actively pursued, but at least you have a defense if you own the game, which can be a mitigating factor).