Your presumption is correct, the top level project being pom packaging should have no source.
So start by removing (just delete or move elsewhere) the src folder from the top level (and everything under it… main, java, resources, text…)
Now, looking at your modules, they look correct. You can test they are configured properly by control-clicking them from the top pom, and they should navigate to the child pom’s.
Lastly you want to set up a source structure under the child projects (which have war packaging). Manually create a folder structure under Employee module src\main\java, right click it and choose Mark As -> Source Root.
Do same for SkillSet and you’re done.