well using the answer in another suggested post, which was to do
<base href="/" />
in the index.html file. This actually made the sub directories in my pushState work! just it was suggested.. but then in return it broke my IE, but i fixed it by putting extra code in my INIT of backbone
Backbone.history.start({ pushState: Modernizr.history, silent: true });
if(!Modernizr.history) {
var rootLength = Backbone.history.options.root.length;
var fragment = window.location.pathname.substr(rootLength);
var search = window.location.search;
Backbone.history.navigate('/#' + fragment + search, { trigger: true });
} else {
Backbone.history.loadUrl(Backbone.history.getFragment())
}