Hi,
Bootstrap doesn't really come with anything suitable for a menu in a cms, so you'll need to figure out your own menu style. A cms by nature can have any hierarchy of pages with any depth and asp.net menu controls also support this hierarchy in that the site map is a hierarchal data source and the menu and treeview controls are designed to data bind to a hierarchal data source.
You can control the css classes rendered on menu/treeview items from theme.skin (study a few different skins and look at the menu and treeview stuff in theme.skin) and you can control the hierarchy structure by the parent page relationships in the cms. ie if you only create root level pages then it will just be single ul with li elements (and you could possibly get away with bootstrap menu css in that case), but as soon as you create child pages then naturally other uls must be nested within the li elements of the parent ul on down to any depth level.
The lack of anything really suited to unlimited menu depth and arbitrary page hierarchy that can be created in a cms is why I had to use something else for the menu in the example bootsrap skins, because I cannot expect that people will limit their site to root level pages.
Hope that helps,
Joe