I actually just overwrite anything I want to change in the site.css, you should load the site.css after bootstrap so it will overwrite the classes. What I have done now is just made my own classes with my own little bootstrap theme. Little things like this
.navbar-nav li a{
color: #fff;
font-size: 15px;
margin-top: 9px;
}
.navbar-nav li a:hover{
background-color: #18678E;
height: 61px;
}
I also changed the likes of the validations errors the same way.