Copy the .nds file and downloader.txt to the flashcart, edit the downloader.txt to reflect the file's location and name on your webserver/fileserver. If you don't have a webserver installed you can simply use AnalogX's SimpleServer WWW app.
Edit: Oh, and pressing B at any time during transfer will cancel and reset the DS. After the download completes you can press A to reset the DS.
So this can be configured to download multiple ds files that are on the web server?