Legendary Enchantment — Background
Commander creatures you own have "At the beginning of your end step, if a source you controlled dealt 5 or more damage this turn, create a 4/4 red Dragon creature token with flying."
If something refers to your commander while you have two commanders, it refers to one of them of your choice. If you are instructed to perform an action on your commander (e.g. put it from the command zone into your hand due to Command Beacon), you choose one of your commanders at the time the effect happens.