If you are lugging the engine, car will let you know. If you are driving a stick (for a while), you will be paying attention to all the clues that the car is giving to you.
Generally, you stress the engine if you are trying to accelerate in too high gear. Usually, it is not a problem when are you decelerating, although there may be cases of some engine/drive-train combination where it would start bucking at low speed and then you need to avoid it by putting in the neutral.