As far as I know the individuals and missile unit ratios are on an army basis, not per allied faction in the army. In other words you could have one Firstborn individual in your Tribe of the Dawn army and all your warbands be from the SoK list. I could be wrong, but the note in the SoK section for the Tribe of the Dawn and Shadow Tribe, indicating that "Restrictions for purchasing Missile Weapon Warbands and Individuals still apply." is there to point out that you can't use the allied troops to ignore the rules for the normal limits. In other words you can't used it to get more than one idividual per warband or more than 40% missile weapon warbands. So you can't have two warbands and two individuals from your TotD army, and then take a Chronomancer and a Repulsar Knight from the Firstborn as that puts you at 4 individuals.
As for unit cards, that is the similar, you don't have to specify which unit cards are for Firstborn and which are for SoK to your opponent other than in the normal way for revealing them. You use all the same type of card backs. If your army is SoK, then use all SoK cards.