I'm not sure what you mean by "controlling" the banners. Bootstrap works in conjunction with the base Zen Cart Banner Manager and its associated configuration settings. If a 'base' banner is enabled, Bootstrap enables multiple banners to operate as a slideshow.
The menu bar at the very top normally only has a "Home" and "Login" link, possible with either a search icon or search mini-form to the right. When you add something to the cart, the "Shopping Cart" and "Checkout" links show up.
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