G'day Razorbacjac
It sounds like you've worked it out, but here's a Plain English version to go with the Barkerese version in the rules.
If you have an army with regular sub-generals, you decide at the start of the battle which command's general gets the highest PIP dice, which one gets the lowest PIP dice, and which one gets the one in between. Throughout the battle, as you roll the dice, one command always gets the highest PIP dice, one always gets the lowest PIP dice, and the other gets the one in between.
You can change the allocation during the battle if you want, but it's messy - in the first bound of the new allocation, all moves cost extra PIPs.
As a result, the rules strongly encourage you to design regular armies with the PIP allocations in mind. Take, for example, my Alexandrian Macedonian army. Alexander commands the Companions, the Hypaspists and a few other support troops, and his command is the army's strike command. So he gets the highest PIP dice. Parmenio commands the Thessalian cavalry and some more support troops, and his command is the defensive wing. So he gets the middle PIP dice. In the middle of the army is Craterus's pike phalanx. All it does is head straight forward to pin the enemy army, so all he needs is the lowest PIP dice.
Now if you have irregular generals, or regular ally generals in your army, those commands roll their own PIP dice, and those PIP dice aren't ever placed in any allocation. The same goes for commands which are off table flank marching, which have lost their general, or which are broken.
I hope this helps, but if you have any questions, please ask us. We're happy to help.
Cheers
Peter
PS Welcome to the forum, I hope you enjoy yourself and the rules. By the way, do you mind me asking you where you live?