Takes some time to understand how the cards work with each other
In practice, it isnt that hard to play them both together because you can usually find a third colored source to get it onto the battlefield, or enough pips early to use Nykthos for three colored mana, or else its just powerful enough with the three extra pips to be worth that minor inconvenience
Theres a lot of sacrifice fodder available to throw -1/-1 counters around, and the proliferate ability can help you to speed up sagas, kill bigger creatures with the previous ability, and grow some of your own creatures
It looks as though we will be getting a whole new lineup from the new Avatar: the Last Airbender set coming later this year
For other purposes, however, if a card refers to your commander, it means either the legendary creature or the legendary Background enchantment