Hi,
look at
http://getbootstrap.com/javascript/#scrollspy
"Resolvable ID targets required!
Navbar links must have resolvable id targets. For example, a <a href="#home">home</a> must correspond to something in the DOM like <div id="home"></div>."
So your links in the navigation should have a target to your 'scrollable' content. Default you have <a href="/link/to/something" ../>
This should be modified to <a href="#content1" ... />, <a href="#content2" ... /> etc.
And in your content you need some divs with this id's
<div id="content1">...</div>
<div id="content2">...</div>
Ok now the solution....
1. Go to your menu (joomla menu)
2. Change 'Menu Item Type' to 'External URL' (see image) and add the target id of your div (step 3) in section 'Link'.
Don't forget to add '#'!
3. Now you need to add the div with your target id in your content
<div id="content">
......
</div>
Repeat this for all menu items (use different id's as target) and include all divs to your content (article, module, ...)
P.S. <body data-spy="scroll" data-target="#t3-mainnav"> was already added by you...
Good luck,
Eugen