The process for packaging a code-based project for HTML5 is actually a little bit simpler (in my opinion). To package a code-based project, you would need to build the project in Visual Studio using the Development configuration for Windows, then open the project in the Editor and make sure to open each map that needs to be included in the HTML5 package. Then close the Editor and go back to Visual Studio and build the project using the Development configuration for HTML5. Open the project in the Editor again and launch it to Firefox Nightly. As I mentioned though, this process will be getting a lot smoother soon.
I believe this process only needs to be run through one time. After the first time through, the necessary HTML5 files should already be in place for future projects. In order to verify this though, I would need to remove and re-install the Engine. That will take me some time to complete.