In the editor you can assign checkpoints with keys 1, 2, and 3, and you can assign InSim checkpoints from menuitem Marshall/Insim checkpoint.

What is the difference between these two? So far I have not used Insim checkpoints at all. What is the benefit of those?

Interesting enough, autocross.txt document in Docs folder doesn't say a word about Insim checkpoints.

Not sure,but I would guess that insim checkpoints just triggers an insim packet (where the use of it is decided by creator of the insim application),while actual checkpoints needed for laptime counting without any insim help.

Quote from lucaf :

Insim checkpoints.

https://www.lfs.net/forum/post/1902845#post1902845

Came into same conclusion. So maybe could be good idea to add also Insim checkpoints into same place than basic checkpoints?

If you have an InSim which has the potential to handle it (LFSLapper), or program your own InSim. Otherwise it's not really doing much.