Hi Peter,
The "Main Menu" is for CMS pages, it would not be appropriate for feature specific edit pages.
How you make a menu for supporting pages in a custom feature is open ended, you can do it any way that works for you. For a simple example look at WebStore it has a link for Store Manager in the title of the module instance that links to a main menu for web store, that men is also a supporting page of webstore it is not part of the main menu. As with any supporting page in a custom feature the pageid and moduleid are passed in the url to all the menu links.
Note that these ideas are for features that plug into cms pages, bu tnot everything one builds to extend mojoPortal needs to be a cms plugin. It would be your own judgement whether something for customer tracking should or should not be a cms plugin. You could build it as stand alone pages outside of the cms system (and outside the main menu) and plugin links for it in the administration menu instead.
Hope that helps,
Joe