Make cakes: Finely chop 3 oz. bittersweet chocolate and place in a medium bowl; set over a pot of simmering water. Add cream and stir until melted. Stir in almond extract.
Refrigerate for 25 minutes, stirring occasionally, until cooled and thick enough to scoop with a spoon.
Sprinkle cocoa powder onto a large piece of waxed paper. Using a teaspoon, scoop mixture into 12 evenly sized balls and drop into cocoa. Roll into rough balls, coating evenly with cocoa. Freeze truffles while preparing cakes.
Preheat oven to 400°F. Grease 12 (6 oz.) glass custard cups or ramekins with shortening and dust with cocoa powder. Tap out excess. Place on a large rimmed baking sheet.
Chop remaining chocolate and butter into small pieces. Transfer to a large, microwave-safe bowl. Heat for 3 to 4 minutes, stirring at 1-minute intervals. Whisk until smooth. Whisk in confectioners' sugar, vanilla and flour, stirring until smooth. Whisk in yolks and whole eggs one at a time.
Divide batter among cups. Put one truffle in each cup and push into center of batter. Bake until tops are set but slightly jiggly, 15 to 17 minutes.
Make sauce: Combine cherries, their juice and sugar in a saucepan. Bring to a boil over medium-high heat. Mix cornstarch and Amaretto; add to cherries, stirring until sauce is thickened and shiny.
When cakes are done, remove from oven and allow to sit for 1 to 2 minutes. To serve, spoon 2 to 3 Tbsp. sauce onto dessert plates. Run a knife around each cake to loosen; invert cakes onto sauce.