To make the cake:
Set a rack in the middle of the oven and preheat to 350 degrees F.
line the bottoms of muffin pans with muffin paper liners.
In a medium bowl, whisk together the flour, baking soda, baking powder, and salt. Set aside.
In a standing mixer with the paddle attachment, beat the butter at medium speed until smooth, about 2 minutes. Increase the speed to medium-high and slowly add the sugar. Continue beating until light and smooth, about 4 minutes. Turn the mixer off and scrape down the sides of the bowl with a spatula. Add the cocoa powder and vanilla and beat at medium speed for 1 minute more. (Stop the machine and scrape down the sides of the bowl again, if needed.) With the mixer running at medium-low speed, add the eggs, one at a time, beating for 1 minute between each addition. Scrape down the sides of the bowl.
Add water and milk in a saucepan and bring just to a boil. Remove from the heat. and set aside.
With the mixer at low speed, add the flour mixture, about a 1/4 cup at a time. Carefully pour the hot liquid into the batter. Remove the bowl from the mixer and, using a spatula, finish combining the batter until smooth. Lightly drop into muffin liners. in muffin pans.
**Insert 1 cherry into the center of each cupcake**