Sprinkle yeast over milk and set aside for about 10 minutes. In a large bowl, whisk together flours, baking powder, baking soda, and salt.
Make a well in the center and pour in oil, honey, and yogurt. Lightly mix. Add in milk-yeast mixture and mix until dough comes together. Dough should be soft but not quite sticky.
Knead for 7 minutes, adding a bit of flour if necessary. Set aside and allow dough to rest for 2 hours. Dough will slightly expand and become stickier.
Divide dough into 6 equal pieces. Roll out on a well-floured surface roll out dough. Thicker naan bubbles less when cooking as compared to thinner naan.
Heat a large cast iron skillet on medium-high heat until hot. Add a little spoon of ghee to the skillet. Place one round on the skillet and cover with lid immediately. Allow to cook for 1-2 minutes. Naan will begin to bubble. Flip naan over and cook for another minute.
Remove from heat. Repeat until all naan dough has been cooked.