Really, as to what you do, I think it mainly depends on what your plans for them are. Most of my seedlings when I potted them to 6" pots, I just potted up "as is" - no pruning whatsoever. I only have a couple that I have tried root pruning and one of those I also snipped the main growth tip all the way back to where it had several small side branches just above the swelling of the caudex.
I don't think there is anything you necessarily *need* to do, it mainly depends on what you *want* to do.
