Hello!
About the barriers, Auto-Barriers are based on the total Initiative count of your 4 ninjas, the one who has the higher total Initiative will activate his/her barrier last. In that way, the one who has the highest Initiative or the last one who activates the barrier will have the advantage. Now for the Manual Barriers, it is the same rule that applies as who has the highest Initiative for that specific ninja, and that's a matter of timing and strategy when it comes to PvP battles.
Note: Madara Uchiha [Edo Tensei Release] is a bit different, no matter what the case, he will use his Barrier last.