Lets say that the chakra rods are mainly to bring each body to life, and each body has a mind partially controlled by Nagato.
God realm being his friend probably goes along willingly, the others are more slaves then puppets thus why he has to order them around.
This would also explain why ino's clan was amazed at him being able to control so many body's at once. In other words he is not controlling them fully so that he can control all 6, then give them orders from god realm to fill in the gaps of the puppeteer work.
The fact that they can all see from each others eyes would explain all the coordination without orders during a fight.
Just a rough idea that needs polishing but ninjas are about tricks and techniques. He very well could be combining several elements to pull off the six paths in the first place.
Kinda like in the cartoons when a head falls off a character and the body can't find the head because it can not see but fumbles around under orders from the head. That is how i see Peins six paths puppet control, The actual Visual help that allows him to move them around properly comes from rinnengan.