The go to answer is to tag both the runners and let the umpire sort it out. But if the defense knows which runner will be called out, he should tag the other runner and say, ”
You’re out.” Maybe he will move off the base and you’ll get a double play.
The umpires should immediately call the trail runner out when that runner is tagged. Shouldn’t be any amount of sorting out needed, unless the coaches want to complain about it.