my mother-in-law to be uses a deep muffin pan to put the sponge mix in, then pours the jam/melted choc/toffee over it just before cooking so it sinks through as it cooks. She makes the best cakes i have ever had (think 12 egg mixes!) or if you want it in a lump do it post cooking, like butterfly cakes.

make ganache. use a piping bag and inject it into the middle of the cupcake just as it comes out of the oven. if you use a pastry back this is a super easy process. there are many easy ganache recipes but the most basic is a 2 to 1 ratio of chocolate to cream. heat cream to almost boiling. pour over chocolate and let the heat melt it. stir lightly to even heat distribution. use quality chocolate. if it's cooled down but still lumpy put mixture on double boiler until evenly melted. when this mixture is cooled and hardened you can also use it for truffles. melon baller- roll in cocoa, etc.

p.s. in order to pipe from a pastry bag the ganache should be cooled a little bit so it comes out like a frosting and not super liquid sauce. it's much easier to control that way.