Edit hover options for edu-clean theme?

Hello!

I am working on getting the edu-clean theme customized for my site, but I've noticed that when you customize all the colors that the "hover" functionality goes away. In other words, if you use it "out of the box" the navigation menus/logo have the hover functionality, but once you change colors there is no place to add hover options in the theme options section.

I am fine with making code edits, but I'm still learning and have no idea where to do this. Can someone please guide me to the section to add hover options for the logo (I realize I'll need to create/load and hover logo image) as well as the navigation menu items? I would really appreciate it!

Thanks,
Amy