Pause at ToD
SmartCARS 3 features a Pause at TOD toggle button which will pause the simulator when smartCARS 3 think it's time for you to descend. This may not be 100% accurate, but it is a decent way to ensure you don't forget to return to the cockpit when it's time to do things.
Simply toggle on the option. When the sim reaches TOD, smartCARS 3 will pause the sim. You'll then be able to unpause from smartCARS 3.