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Once the top level menus are setup, will it automatically update subcategories (if say, new subcategories are added?)

Yes, it will automatically update and setup. There is no separate page to manage for mega menu navigation, you can see our mega menu tab in the Magento default category page in admin. Then, simply select mega menu settings for the main categories and that's it. Please check out the demo for more details http://magento2demo.rootways.com/admin_2fh5c1/
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