Making pierogis from scratch is an undertaking - one that is totally worth it! Slideshow: More Russian Recipes
In a large bowl, stir together the flours and 1 teaspoon salt. Beat in the eggs and water with the handle of a wooden spoon, then continue to knead the dough with your hands until a smooth and elastic dough has formed, about 10 minutes. Wrap the dough in plastic wrap and let stand at room temperature for 30 minutes.
In a medium heavy pot, cover the potatoes with salted water and bring to a boil. Boil the potatoes until very tender, about 20 minutes. Strain and reserve the potatoes.
While the potatoes cook, in a large heavy skillet, heat the oil over medium high heat until hot. Stir in the onion and 1/2 teaspoon each salt and pepper, then cook, stirring occasionally, until golden, about 6 minutes. Add the potatoes to the skillet with the onion and mash together until smooth. Season the filling with salt to taste. Let cool to warm.
Halve the dough, keeping one half wrapped, then roll out the other half of the dough on a floured work surface to a 14-inch round. Using a 2-to 3-inch round cutter, cut out rounds from the dough. Place a scant tablespoon of the filling on one half of each round of dough, then moisten the edges of the rounds with water and fold into half moons. Repeat with the remaining dough and the remaining filling.
In a large pot of boiling salted water, cook the pierogi in batches until tender, about 12 minutes per batch. Transfer the pierogi with a slotted spoon to an oiled baking sheet.
In a large heavy skillet, heat 2 tablespoons of the butter over medium heat until hot, then brown the pierogi in batches, adding additional butter as needed. Serve the pierogi with sour cream and chives.