when i log out ill have 1 character in the main slot
but when first run starts it will have the characters in different spots
for now i start first run and when it gets to the character screen
i note where it has them and then exit and set the option for main/left/right accordingly,
is this just how i have to do it o is there some way to tell
what slot its going to show the characters in beforehand?

if i change setings like tractor beam range or max approach distance do i have to
re-run the first run option or will they adjust automatically when i log in with the looter?

Option main/left/right works during first run only. You do this correct. Need to define what is the default position of a character during first run and set it in settings.

You need to rerun first run if you want to change any setting in game, like window positions, overview settings, hotkeys, new window (drones present or absent). When you switch type of a laser (or anything else which just changes numbers) you dont need to rerun first run.