We're (probably) going to be using a special module for the megamenu. It allows you to display blocks within the menu, but only blocks that are active. So we're probably going to set up a dummy region for menu blocks, which won't be rendered in our templates, but that will satisfy that module's requirements.
Soo.... To add a block to the menu, you need to add it to the menu blocks region in order to make it available to the menu module.