Ideally you'd use the override support in Ext.define:
It's a little counter-intuitive but the code above does not define a new class, it overrides the existing class. By using this style of override it fits more naturally into the normal class-per-file structure and can be included using the loader.
As for what name to give the override (in my example I just switch Ext to MyApp) I'm not sure whether there's any official advice on that. Personally I don't like mixing overrides with my application code so I tend to name things in such a way to keep them in a different part of the source tree.
Occasionally I do use the one-big-patches-file approach though I'm pretty sure that's not encouraged. In that case I don't try to load it dynamically, I just script tag the patches file directly into my HTML.