When working with the navigation bar in Twitter Bootstrap, remember that it is essentially just an unordered list. Feel free to organize your code neatly or messily, but ensure that you create a div with an id and a runat="server" attribute, and reference it in your code behind. Here is an example of how your markup could look:
<div id="myNav" runat="server"/>
In the code behind, retrieve your data items from the database, generate the appropriate HTML, and then write it to the DIV. Consider the following code snippet:
Dim sb as New Stringbuilder()
sb.append("<ul>")
sb.append("<li>Item 1</li>")
sb.append("<li>Item 2</li>")
sb.append("</ul>")
myNav.InnerHTML = sb.ToString()