In an airtight jar, combine the cherries and rum. Add enough rum that the cherries are covered but not drowning, or you'll end up with too much liquid. Shut tightly and keep in the fridge for at least 12 hours, upto 24 hours.
To make the cakes, first sift the flour and baking soda in a large bowl. Set aside.
Preheat the oven to 175 C and line 16 muffin moulds with cupcake liners. If not using cupcake liners, generously grease the moulds.
Melt the chocolate till smooth in a double boiler or heatproof bowl set over a pot of simmering water. Set aside to cool.
In a large mixing bowl, beat the butter and sugar till pale and fluffy. Add the eggs and vanilla and beat well. A hand mixer is best here.
Add the melted chocolate, and mix till combined but do not over-mix.
Now add the flour mixture gradually, alternating with the boiled water. Stir gently, avoiding lumps as much as possible. If you do see any lumps, run a hand mixer through the batter. The batter should be smooth and a little runny.
Finally fold in the boozy cherries and pour in any rum left behind. Mix well. The batter will be thinner now so don't worry.
Divide the batter equally among the muffin moulds and bake for 20 to 25 minutes until they have risen, developed crackly tops and a toothpick poked in the center comes out with only a few moist crumbs. Start checking for doneness at 20 mins as all ovens are different.
Allow the cupcakes to cool in the tray for 10 minutes and then place them on a wire rack to cool completely. They might sink as they cool, this is normal for a fudgy cake with extra moisture.
In a small bowl, lightly beat the mascarpone, sugar, cream and vanilla till smooth and fluffy. You don't need a hand mixer here, a spoon is enough. Dollop small amounts onto each cake and serve with more fresh cherries! Store refrigerated for 4 to 5 days.