Hi @soumya5 ,
This is very easy to do, just go to the Taxonomies module in the Content Taxonomy app, where you should find the default taxonomy (i.e. topic structure) called 'Employee'. You may want to clone it before introducing any changes so you can always easily refer to the default version.
You will see all mega-menu topics as "child topics" under the taxonomy and then when you open any given one, they will have their own child topics, e.g. HR will have Benefits, and this in turn will have its own 4 child topics (as shown in your screenshot) and so on. As an example below you can see the child topics for the IT mega-menu topic:
I believe the topics only show in the menu when they have child topics or "connected content" (first tab in the screenshot above), which is the actual items you want to display in the given category, e.g. catalog items or knowledge articles. Make sure the topics are active and have a value in the order field as well.
Finally, make sure the default taxonomy is disabled and your new one is the only active one.
