For questions and problems with the CMS core. This board is NOT for any 3rd party modules, addons, PHP scripts or anything NOT distributed with the CMS made simple package itself.
The short answer is yes, you can have more than one menu. But you need to learn how the menus in the templates works.
See help in MenuManager, and also Default Templates Explained.
The menus in CMSMS is normally generated upon the page structure. You can also set up a menu that only shows certain pages, for instance by using the includeprefix parameter, or by using the items parameter containing only the pages you want to show. Or you can make menus that dont' show certain pages, using the excludeprefix parameter. You might also set up menus that starts on certain positions in the hirearchy by using the start_page parameter or the start_level parameter.
With good planning of pagestructure and using these possibilities, you might be able to set up a system that generates the menus you need automatically.