Line 2 muffin tins with cupcake liners (24), and set the oven to 350 degrees. Scoop batter into baking cups, filling cups about 3/4 full.
In the mixing bowl of a stand mixer, and using the whisk attachment, on low setting, mix the Flour, Cocoa, Baking Powder, Baking Soda, and Salt. make sure all ingredients are well blended.
Add, Oil, Eggs, Sugar, Vanilla, and Milk, and keep the mixer on low, and blend all ingredients together until the batter is smooth. Turn the mixer on high, and beat for 1 minute.
Bake the cupcakes for 16 - 18 minutes, or until a toothpick comes out clean.
When the cupcakes are done, remove them from the oven, and place them on wire racks to cool completely. When cupcakes are cool, with a cupcake corer, remove the center of the cupcake, and keep the center pieces, DO NOT DISCARD CENTERS. (I simply lay them next to the cupcakes).
When centers have been removed, place a chocolate covered cherry in the center and then place cupcake center back in cupcake; it will stick up a little, but that's okay because the frosting will cover it.