I know that this can be done from the command line, but I can't seem to find a way to change the Application Administrator password from the GUI. I can't find a "users" menu.
I believe this can only be done via cli. I don't know why the docs don't really highlight this fact, but you will see it somewhat hidden in notes like the one below;
Troubleshooting Tip
You set the Administrator username and password during IM and Presence installation, and you can change the Administrator password or set up a new Administrator account using the Command Line Interface (CLI)