Currently when you open a web map in ArcMap in 10.0 or the upcoming 10.1 release, it gets converted to an ArcMap map document. Your map document contains the same map service layers as the web map and starting at 10.1, layers that are based on map notes or uploaded files get converted into file geodatabase feature classes that you can immediately work with. There's no automatic connection back to the web map in ArcGIS Online. Any changes that you make to the map you opened in ArcMap are just stored locally in your map document. So if you delete or add layers, or change how the service layers are drawn, that isn�??t reflect in the web map.
Having a subscription is what will allow you to publish your data into ArcGIS Online. From ArcGIS desktop, you'll be able to take your map documents and create web services out of them--initially, tiled map services and feature services.
Thanks,
Mike