For checkpoints you need two things.
1. Insert the checkpoint box and set the object type to 'checkpoint'. The start/finish line should be the highest checkpoint number. If you find the checkpoints are not in the order you want, just go through them in traxx, one by one, in order, and manually enter the checkpoint numbers in the object properties box. Checkpoint models are invisible in the game.
2. A checkpoint marker so racers will know where the checkpoints are. This can be a flag, or a pole, or a banner, or anything you like. Just insert the marker like a normal model beside the checkpoint box. Some people like to set markers as no-collide so they don't interfere as you go through the checkpoint.
More info here
http://cownap.com/~traxx/traxxld.html