How to create a checkpoint system in minecraft

At the respawn of your game, put signs down that resemble these so the player knows to only go here if they have died already.

Wherever you want a checkpoint, put an iron door down, a lever, and a sign next to it instructing the player what to do. Then dig straight up from that spot and put water at the bottom.

Make a tunnel to the checkpoint hole, or to the door if the checkpoint is above ground. Place a sign telling the player which checkpoint it is.

Tell the player what to do if they came down to try to get ahead. You can make a ladder back to the top but I was a bit harsher.