I always tell coaches before we start that if they sub, have the kids go to the table, check in and then wait to be called in. Also, they must have their jerseys tucked in. If they're not tucked in, they will have to play the rest of the game without jerseys and with their number written on their forehead in permanent marker.
They usually remember to tell their players to have their jerseys tucked in when reporting.
Oh yeah, I only make the "no jersey" threat in boys games.