As stated in the Bootstrap docs, you have to define the CSS classes for nav and navbar for when the affix
kicks in...
"You must provide the styles for these classes yourself (independent of this plugin). The affix-top class should be in the regular flow of the document."
So you'll need to have some CSS for both the top navbar and side nav..
#nav.affix {
position: fixed;
top: 0;
width: 100%;
z-index:10;
}
#sidebar.affix {
position: fixed;
top: 80px;
}
Here is a Bootply demo using affix
with both top and side nav: http://bootply.com/69848