Install AutoHotKey and activate the .ahk script through AutoHotKey. Alternatively, download and run the pre-compiled .exe for 32bit/64bit architecture, which already contains the AutoHotKey ...
NOTE: Make sure your 3DS and the computer you're using beeShop on are on the same network, if they aren't, you will not be able to send the files over to your 3DS. beeShop should now start downloading ...