main.js

YUI({
    combine: true,
    modules:  {
       'my-module': {
           fullpath: "my-module.js",
           type: 'js',
           requires: [ "event","event-custom","event-valuechange" ]
       },
       'my-module-2': {
           fullpath: "my-module-2.js",
           type: 'js',
           requires: [ "history","io","json-parse","node","node-event-simulate" ]
       },
   }
}).use("my-module", "my-module-2", function(Y) {

     //Now my-module, my-module-2 and all of their dependencies are loaded.

});

me-module-2.js

YUI.add("my-module-2", function(Y){
    Y.MyModule2 = {
        init:function() {
          Y.log('my module 2 inited');
        }
    };
}, "0.1");

my-module.js

YUI.add("my-module", function(Y){
    Y.MyModule = {
        init:function() {
          Y.log('my module inited');
        }
    };
}, "0.1");