UPDATE: version 1.0.1 released
I've released a new version (1.0.1) of the menusystem library, which is now called arduino-menusystem. This update includes a fix for the buffer overflow mention in this thread, which also means that there is no longer a limit of five items per Menu - they are now dynamically allocated, so you can have as many as your arduino can support in it's little memory.
As the name has changed, so has the github link: GitHub - jonblack/arduino-menusystem: Arduino library for implementing a menu system
NOTE: The arduino IDE has a hissy-fit when loading the library because the project now has a dash in its name. You can rename it locally without it being a problem, just remove the dash. I have no idea why the arduino IDE cares about this, but I'm not changing the name 
@niesteszeck
As much as I wanted to I couldn't find a generic way to implement a setup menu item. My first thoughts were right on this. I've been writing a clock using an LED matrix, and I solved this by using the menu to change a global variable called "current_mode". Depending on the mode, different things are displayed on the screen and the buttons do different things. When in a mode for setting the display brightness, the buttons change the value of another global variable. I hope this helps.