After running the installer (or any exe) bottles scans the registry for certain keys (I don't know the specifics) and if it finds that new programs have been installed, it automatically adds an entry under "Programs" in the Bottles UI (which is under the "run executable" button).

You also have the option to manually add installed executables under the "Programs" section, or into the "Library" section (Library is global, programs is per-bottle-sandbox)