With manual your mystery skills of ninjas in your team will target the one selected. The automatic attacks will target people in front of them.
I understand its the higher difficulty fight that your having trouble with and thats where I recommend using manual on if your struggling. And as mentioned before, if you use ninja war kiba, ino, shikimaru you will have chaos on hidan every turn, he will kill his own team. You c*so interrupt his skill with your main whenever he uses it. AI is pretty predictable and follows a pattern. You will see in which round who tends to use a skill from the enemy team and then just interrupt it once you know their order.
And if your really struggling even while trying everything, just get more power first before you try again. You do not really need the 3 battle points anyway untill your 70 when you can get tsunade. That 1 extra battle point will not make a difference untill then.
Also when it comes to pve you will have to adapt to the enemy team. Especially when it comes to ninja exam. There is plenty of threads with tips on how to beat certain ninja exam stages more easily. In survival trial I recommend using a team with sustainability that can get you through many missions without losing ninjas. Then use more ninjas on the last fight and breakthrough fights if they are too hard for you. Guy, naruto and gaara are pretty strong in survival trial because naruto : clones tank damage, guy: everyone gets life leech, gaara: gets shield every round so doesnt lose much hp inbetween fights. note: dont use them all in the same team, just using 1 or 2 is fine. On your main take the 3rd skill that shields 2 people every turn.