Am I playing the Hero Limitation rule correct.

300 point Army, I am allowed maximum 2 platoons and a maximum 2 Heroes for my army. The 2 Hero Maximum inlcudes a Hero that I have as the Command Section. The only way to have a third Hero in a 300 point army would be to pay 5 AP plus the cost of the Hero in the Allied build?

Thanks for any clarrification.

Yes that is correct. If you take a hero as your command section it still counts towards the hero limit.