I think the core bootstrap classes should not be styles over. FOr example in core Jooml template for
<div class="container">
you use
.container {
background-color: white;
-moz-border-radius: 4px;
-webkit-border-radius: 4px;
border-radius: 4px;
padding: 20px;
border: 1px solid rgba(0, 0, 0, 0.15);
-moz-box-shadow: 0px 0px 6px rgba(0,0,0,0.05);
-webkit-box-shadow: 0px 0px 6px rgba(0, 0, 0, 0.05);
box-shadow: 0px 0px 6px rgba(0, 0, 0, 0.05);
}
But container is used in many other places. FOr example in nav bar. You can find it in Responsive navbar BS example.
So if I try to use it I get
I think it have to bee separate class.
<div class="container main">
and give this stiles for main frame of the site to
.container.main