Hi Stephen,
If the cb menu is displaying instead of the main one, just login to joomla as administrator, go to the menus area and make the main menu ( or whichever menu you want to use) the default home. Then add menu items to the default menu as you wish.
CB never overwrote the menus on my site. Not sure how that could happen.
If you can't access the admin area, that's different and could mean you accidentally locked yourself out. Let us know how it goes?
Good luck,
Satchi