Preheat oven to 350 degrees. Line 24 cupcake molds with paper liners. Set aside.
In a large stand mixer bowl, add sugar, flour, cocoa powder, baking soda, baking powder, and salt on low until completely combined. In a separate medium bowl, whisk together eggs, egg yolk, sour cream, milk, and vanilla until completely combined.
With the mixer on low, slowly pour in wet ingredients into dry ingredients. Mix just until all lumps are removed and the batter is smooth. With the mixer still on low, pour in the hot brewed coffee. Mix until completely combined.
Using a cookie scoop, scoop batter into each prepared cupcake liner until 2/3 full. Place filled cupcake pans into prepared oven and bake until a tooth pick comes out clean when inserted in the center. Remove from oven and let them cool in the pan for 5 minutes. Remove cupcakes from the pans and let cool on a rack completely before filling.
While the cupcakes cool, make the filling. Add cherries, amaretto, sugar, and cornstarch to a medium sauce pan and stir together. Place over medium-high heat until it starts to simmer, about 3 minutes. Using a potato masher, mash the cherries to help release their juices. Continue cooking until mixture starts to thicken, about 3 more minutes. Reduce heat to low and cook for 2 more minutes. Remove from heat and set aside to cool.
Cut a 1-inch circle in the center of each cooled cupcake and remove some of the filling underneath. Save the filling for later. Place 1 teaspoon of cherry filling into the hole of each cupcake.
Make the whipped cream topping by whipping heavy cream and 1/4 cup of sugar until firm. Place into pipping bag with large round tip. Pipe whipped cream on top of each cupcake.
To finish off the cupcakes, make the chocolate-dipped cherries. To do this, warm the cream in the microwave until scalded (between 30 seconds to 1 minute). Add to chocolate chips and let sit for 10 minutes. Then stir together until completely combined. Dip cherries into chocolate and then place on top of cupcake. Repeat for the rest of the cherries. Sprinkle cupcakes with pieces of cake that you saved from earlier.
Serve cupcakes immediately or place in refrigerator for up to 3 days.