Hmmm, the first battle shouldn't be too problematic, what I imagine is happening is your not selecting actions for each soul puppet.

You need to click just under a puppet and select a move from the dropdown at least, even if that move is just "attack", and then maybe which enemy creature your going to target, though generally selecting attack will attack the first enemy in the enemy party first so you only need to worry about targets when playing tactically.

The main thing however is if you don't select a move, your soul puppets will do nothing while the enemies attack you which obviously is a great way to lose battles.

If you have premium option you can use a hotkey to set all soul puppets to attack which can speed the process up, I don't recall which key that was off hand as I didn't use the keys much I just clicked with supernova instead.

As I said, puppet nightmares has quite the learning curve but it's well worth getting into.