Here's an example how to define prefixes for YepNope.

yepnope-prefix-path.js

/*
 * Get paths to the js files to use in yepnope
 * window.thePath is defined in footer
 */
(function(yepnope) {

    // Domain name
    // var domain = window.location.host,
    //     origin = window.location.origin;

    yepnope.addPrefix('pathBower', function(resourceObj) {
        resourceObj.url = window.thePath + "/lib/" + resourceObj.url;
        return resourceObj;
    });
    yepnope.addPrefix('pathScripts', function(resourceObj) {
        resourceObj.url = window.thePath + "src/js/" + resourceObj.url;
        return resourceObj;
    });
    yepnope.addPrefix('pathStyles', function(resourceObj) {
        resourceObj.url = window.thePath + "/css/" + resourceObj.url;
        return resourceObj;
    });
})(this.yepnope);