1) Preheat the oven to 350°F. Line two 12-cup muffin pans with cupcake papers; spray the papers with vegetable oil spray.
2) Beat together the butter, sugars, and salt until fluffy and light, at least 5 minutes, scraping the sides and bottom of the bowl.
3) Add the eggs to the butter mixture one at a time, beating well (at least a full minute) after each addition, stopping to scrape the sides and bottom of the bowl before adding the next egg.
4) Mix in the vanilla.
5) In a separate bowl, whisk together the flours, cocoa, and baking soda. If lumps remain, sift or strain.
6) Stir half the flour mixture into the batter; then the yogurt and water; then the remaining flour mixture, stopping to scrape the sides and bottom of the bowl.
7) Scoop the batter into the prepared pans, using l/4 cup for each cupcake (a muffin scoop is a great help with this).
8) Bake the cupcakes until a cake tester inserted into the center of a middle cupcake comes out clean, 22 to 24 minutes.
9) Remove the cupcakes from the oven, and after 10 minutes transfer to a rack to cool.
10) Frost completely cooled cupcakes, if desired. Our Super-Simple Chocolate Frosting is a great match here.
Yield: 2 dozen cupcakes.