In a small saucepan over low heat, bring the brandy and orange juice to a simmer. Add the cherries, simmer 1 minute and turn off the heat. Soak the cherries in the warm mixture until they plump up, about 10 minutes.
Preheat the oven to 450 degrees F.
Set a heat-proof bowl over a saucepan of simmering water. Place the chocolate and the butter into the bowl and let it sit over the heat until the chocolate begins to melt. Stir to combine and continue to heat until the mixture is smooth and the chocolate is completely melted. Remove from the heat.
In a large bowl, beat together the whole eggs, yolks and sugar until the mixture turns light and thick.
Pour the melted chocolate into the egg mixture. Beat in the flour until just combined. Do not over-mix the batter.
Butter 6 (4-ounce) ramekins. Sprinkle each ramekin with 1 teaspoon cocoa powder and tap out the excess. Divide the batter among the ramekins. Drain the cherries and put a few cherries into the center of each ramekin. Use a spoon to push the batter over the cherries to cover them.
Place the ramekins on a baking sheet and bake for 7 to 9 minutes. The outside of the desserts will be set, but the centers will be soft.
To serve, invert each mold on a plate and let sit for 10 seconds. Slowly lift one side of the mold and the cake will fall out. (If the cakes won't easily come out, just serve them right in the cups.)
DB note: These little desserts are easy to make ahead. Refrigerate them in the baking cups and when you're ready to bake, bring them up to room temperature and bake as above.