Well, an app is just one single program. Internally, the "app" is just a folder ending in .app. Inside it you'll find Contents/MacOS and that is where the single executable is located which is launched when opening the app (e.g. double clicking on the folder). If you have additional command line programs those usually are not apps (you'd have to type open mytool instead of ./mytool to run the command on the command line). If these are just called from the main app you can hide them inside the app folder (maybe Contents/Resources or create Contents/bin). Otherwise, Apple also has installer packages (.pkg) which extract several items (instead of just a single app folder) to their appropriate places. There would be an appropriate place for command line tools and the PATH environment variable should also be adapted to make them visible. But, I don't know how to create .pkgs.
If you truly have multiple GUI programs, these should actually be separate apps.