Place the cherries on some paper towels and let them dry. Melt the chocolate chips in the microwave until they are almost all melted, about 1 ½ - 2 minutes. Stir the chocolate until it is all melted and glossy. Dip the cherries into the chocolate and place on the prepared baking sheet, pressing down a little to create a flat surface. Refrigerate for ½ an hour or until the chocolate has hardened.
Preheat oven to 350 degrees. Line 12 standard muffin cups with paper liners.
In the bowl of an electric mixer, beat the eggs, buttermilk, butter and vanilla on medium speed for 2 minutes. Turn the mixer to low and slowly add the cake mix. Beat just until combined. Divide the mixture evenly among the prepared muffin cups, filling almost full. Bake for 20 minutes or until the tops are springy to the touch and a toothpick inserted in the center comes out clean. Let cool for 5 minutes in the pan then remove to a cooling rack to finish cooling.
Frosting and filling
Beat the cream cheese, butter, salt, vanilla and cherry juice together until blended. Sift in 2 cups powdered sugar and mix to combine. If the frosting seems too soft, beat in a little more to stiffen it. The mixture should be a little thicker than heavily whipped cream.
Take about ½ cup of the frosting and put in a plastic food storage bag. Snip off the end of the bag so you can pipe the mixture into the cupcakes. Refrigerate the rest of the frosting until time to finish the cupcakes.
Cut an inverted cone out of the top of each cupcake about the size of a nickel. Remove the cone and save it. With the end of a wooden spoon (or your finger) gently push the hole in the cupcake to widen it. Pipe a little frosting (about 1 teaspoon) into the hole. Place a cherry on the frosting and then pipe in a little more frosting to cover the cherry. Cut the end off the reserved cone and place it back on top of the cupcake to cover the hole. Repeat with remaining cupcakes.
Frost the cupcakes and place a chocolate covered cherry on top of each, gently pressing the cherry into the frosting.
Can be made a day ahead. To store, keep refrigerated but take out of fridge about 10 minutes prior to serving to take the chill off.