To include your own assets in the upload, put them in the extra-assets subdirectory of the scene directory. You can reference the assets in index.html, head-end.html or body-end.html with $EXTRA_ASSETS/<asset>.
The $EXTRA_ASSETS constant will be correctly resolved in the uploaded scene, but unfortunately not when the scene is opened locally in the desktop application. The next version of the desktop application will include support for $EXTRA_ASSETS.
An alternative to using extra-assets is to host your own assets on your own server.