Search "xdelta patcher" on Google or whatever search engine you use. Download it from Github or whatever trustworthy site. It's probably downloaded as a .zip, so unpack the folder (you don't need any additional software for this (on Windows 10 at least)) and open the unpacked folder. A program called xDelta Patcher or something along those lines should be in it - open that program.
xDelta is pretty easy to use: just select the ROM you would like to turn into a patch (your hackrom, game.nds in this case), select the ROM people who download the patch should apply the patch to (the European ROM version 0022 - (E) (Wet 'n Wild) is most commonly used), and create the patch! It's that easy! You can also use xDelta to apply patches to ROMs.
Once you've created your patch, it's good practice to apply the patch to an unmodified ROM again and test the resulting hackrom so that you test both the hack and the patch. xDelta is stable, but better safe than sorry. If the patch works, you can upload it to Github, replacing the .nds, or you can even upload it directly to Kuribo64's uploader. Oh, and before you ask about the three .nds files in the uploader, those are homebrew, i.e. not based on any official DS software.
Hope this helps. I'm a SM64DS hacker too. I will download your hack and play it soon. I will tell you what I think of it!