In a medium bowl, add filling ingredients and combine well. Set aside.
In a large bowl add both flours, baking powder and salt and mix well. In a separate bowl add the remaining dough ingredients and whisk until combined. Add wet ingredients to the dry ingredient using a wooden spoon to form a ball. Cut in half. (You can freeze dough for another time, if desired.)
Flour a work surface and roll dough about 1/8-inch thick. Use a 3-inch biscuit cutter to cut out 12 rounds from the dough.
Place a dollop of filling in the center of each dough round. Fold dough over filling to form a half moon. Press edges together with your thumb. Seal the edges using the flat tines of a fork.
Bring a large saucepan of salted water to a simmer. Add perogies and cook for about 2 minutes. Drain perogies.
Meanwhile, in a large skillet over high heat, melt half of the butter and add the onion.
Cook onions for 5 to 6 minutes until slightly caramelized. Add perogies and the remaining butter. Allow to saute for a few minutes, then add the scallions.