You went to Appearance > Menus, you created a menu with a certain name, arranged the menu items the way that you wanted, and clicked the Save Menu button?
Did you then click on the Manage Locations tab and select your menu name from the drop-downs, then Save Changes?
I’m not sure if I could understand your question well or not. But if you have problem with main menu order which navigate between pages;
This can done by config the menus.
At left side of page edit, under Page Attributes you can set the order.
You don’t need to set 1,2,3…; and can set bigger numbers like 10,20,30… , So when you add new page, you can choose number between pages easier.