Not sure how to change the marker except to grab it and move it your self.
To get the other items insted of route origin in the scenario creating part, you have to make a GPS marker file for the route with all the starting location you would like to have. RW Tool shas an option to do this for you, but you have to fly around the route in edit mode and use the GPS pull down and copy and paste the coordinates into RW Tools and give it a name. When your done it saves it to your route\templates\markers, not 100% on the names of folders here as I am at work. Then you can use all the entries you made as starting points for a scenario.