Sitebuilder has nothing to do with how your top navigation is created or rendered. This is handled elsewhere in the system and you will have full control on how those links are managed. Sitebuilder simply creates departments, their directory names, and allows you to add the pages that comprise each department. In reality, you could have as many as 50 departments, or more... but you would only have 5-8 links in your top/primary navigation. So, it doesn't make sense to confuse the top navigation with the basic creation of the physical site departments and pages.
It is true however, that the pages you add into each department do dictate the secondary navigation for that department. So, while you are adding them, you will notice you have up/down arrows to the far-right of each item so that you can order them in that departments navigation.