DragonRuby GTK expects its resources to be in the main toolchain folder, but your project folder(s) can be wherever and have whatever layout you want. Personally, I keep all the projects I’m working on in a single folder in the toolchain folder, and move the changelog, ctags files, docs, and samples to their own archive folders. Pretty much everything else is used by the build system.
Within a project, the app (with main.rb) and metadata (with game_metadata.txt and icon.png) folders are required, anything else is referenced relative to the project folder and can be named to your liking, e.g. app/my_classes/some_class.rb or sounds/boom.wav.
The default mygame project folder just has a basic "Hello World" app layout. You can duplicate that as a starting point or create your own layout or template.