When planning a route, is there a setting that ensures that Mapsource saves the waypoints in the order that you actually enter them (as opposed to alphabetical order)
I'm not sure why you would want to do that. Alphabetical is useful for lookup purposes - the important order is in a route which will store them in the order you have sort them into.
To answer your question, there is no setting that I am aware of to tweak the saved order.