Simply download a theme in the releases, and extract it to SD:/3ds/3DiScord/theme/. It's as simple as that!
Download the theme template included in this repo, and start editing the images. This should be really easy!
There are multiple reasons. First, themes provided here come from a trusted source, so you can be sure they won't do anything to your Discord account or your 3DS. Second, themes here are always updated, and will work with the latest 3DiScord version. Third, the themes provided here come as simple files you can extract to your SD without having to reinstall a CIA.