They move the command up and down, so you can change the order in which they are executed.
I wasn't sure I understood you. The commands are within the scenario and are executed when the scenario is activated. Also the buttons are bound to the scenario itself so I can't see how they would effect the commands within it. BUT...your reply did get me thinking of something else, ie..changing the order of something - and it turns out that they actually change the order in which the scenario buttons appear on the orbiter for the room they are created.
One thing to also note is that they cannot interact with the order to the auto-generated scenarios. In other words, the auto-generated scenarios cannot be displaced/moved within the order. they are always first..