When you're figuring out the this year's class schedule, and trying out different iterations of the master schedule, you have the option of copying just hand-placed students or both hand-placed and auto-generated students to each solution copy.
Choose Master Scheduler from the Scheduling drop down menu, click on Master Schedules then select the copy solution button to the left of the solution you would like to duplicate. In the new window make sure to check the Include System Placed Students checkbox. If this box is not selected the system will only copy hand-selected students. Checking this box copies auto-scheduled students as well.