Pages organisation and menu

So I’m making a web site with a number of pages, some of which are supposed to appear on the main menu, and some are not. How to organize the pages so that it can be controlled from the admin panel which pages appear on the menu and which don’t, given that users will be creating the pages and it’s not a fixed number of pages?

One way I figured it can be done is to have all pages on the menu be a child of some Main Page and list only it’s subpages, but then the url of all the subpages looks like mysite.com/mainpage/contact, whereas I want them to look like mysite.com/contact. The Main Page itself is the index page.

Any suggestions?