Now we get to the advanced stuff... The Menu Manager is a module to lets you create virtually any kind of navigation system. There are already three templates with your default installation. For most users these are enough, as a menu basically is just an unordered list that is styled with CSS.
Probably this is all you need to know, use the template simple navigation for normal list menus (what used to be called bulletmenu in previous versions) or cssmenu for dropdown menus. Like this in your template:
But for those who are adventurous or skilled enough, you can customize the menu templates and add new ones with the Menu Manager. You can use either file templates that you upload with FTP or database templates (by importing file templates or add new ones directly to the database).
Menu Manager in the CMSMS Admin Panel
Read more about how to do this in the help for the Menu Manager in the CMSMS Admin Panel. It's found in the Extensions menu.