As you've figured out, if you want to send 2D goals using rviz, you need to set up and run the ROS navigation stack. It's not clear from your description if you already have the navigation stack running or not, but if your robot is doing waypoint-based navigation is probably has something similar running already.
If navigation is already running, you should find the ROS node that is sending goals to it, disable that node, and use rviz to send those goals instead.
If navigation isn't already running, there's a good chance that attempting to run the ROS navigation stack will interfere with the robot's existing point-to-point navigation system. The navigation setup tutorials give a sense for which subsystems are required to run navigation, but if you already have subsystems that are providing those functions you'll have to figure out how to use those instead of the subsystems in the ROS navigation stack, or make them coexist with navigation.
If you don't know how your robot currently works, you should try to get in touch with the person or company who built it and ask them how to do this integration; they'll be far more familiar with it and they'll be able to offer more detailed advice.
