Hi Aaron,
1. When you add a secured service to a Web map in ArcGIS Online, the Identity Manager will detect it's a secured service and prompt the end users of the service for login credentials. Appending the token to the URL when adding the service will not work the way you are thinking. Since the service is secured, anyone accessing it from a web map will have to authenticate.
2. ArcGIS Explorer Online does not support secured services, so the workflow above will only work with the ArcGIS.com Map Viewer and mobile clients.
3. Currently there is not a way to synchronize your changes to ArcGIS Online to reflect updates in the data. The best way to achieve this now is to re-publish the service and selecting the option to overwrite the published service.
Hope that helps,
Andrew