I believe this happens because you launch the software without Admin rights and any change you perform in the application regardless if it's about its functionality or simple window ordering will revert back to the default ones. Therefore, right click the software and choose Run as Administrator, then change all the windows order and position as you please and close the software.
The next time you'll open Draftsman Cutting Shop, all the windows and settings will be restored from the previous session. This is the only requirement. Sometimes apps have a dedicated button that you can use to use Save Settings. Look through the main menu and settings to check it up.