Hi, I was just wondering if you put a Muk and Aerodactyl in your deck and
had both of them in play could you choose not to use one of the pokemon
powers or would they automatically be "turned on" at the same time? This way
I could use Aerodactyl's pokemon power instead of Muk's during one turn if I
choose to do so.

No.  Muk's Power will turn off Aerodactyl's power, allowing Evolutions.

Scott