Prepare cake mix and bake according to package directions for cupcakes. I have included 3 eggs and ⅓ cup of melted butter in the ingredients, but you can also use vegetable oil as the box mix recommends.
Cool completely.
Add lemon filling to a piping bag with an open metal tip. Plunge tip into the cupcake and gently squeeze filling inside. Repeat until all cupcakes are full.
Use a spoon to scrape off any filling that has overfilled out of the hole. You want the top of the cupcake to be relatively flat.
In a saucepan on medium high heat, add heavy whipping cream and beat until almost boiling. Remove from heat and add chocolate. Set aside for 10 minutes. Stir chocolate until melted and mixture is incorporated well. Let set for 15 minutes.
You'll know your ganache is ready when you dip your finger in it and it slowly drips off and maybe a drip even hangs on your finger. If it's not ready it will run off your cupcakes. So if you are not used to using ganache, test it out first. If you are antsy, you can put it into the fridge and wait for five minutes and then check on it by stirring it. You need to check on it every five minutes, because in no time, it will harden and you'll be mad at me. If you over-harden, toss into the microwave for 5-10 seconds, stirring after each segment.
Dip your cupcake, straight down, into the ganache. Set aside and let set for five minutes. Repeat until you have two layers of ganache on each cupcake. Just after dipping the second layer, add zest to top.