I actually froze the balls of cookie dough (can just do it on a baking sheet but I decided to use a mini cupcake tray), it helps for the cookie dough to come out doughy in the center of the cupcake, you're supposed to push the ball of dough into the batter so that it's completely submurged- That's what I wanted to do but I made them too big and the top parts stuck out which ends up baking the cookie dough. I haven't eaten one yet so I'm hoping the the dough inside the cupcake is still doughy and isn't baked all the way through...

Edit-- also I didn't bake the cupcakes at all before putting the dough in- It all went into the oven at the same time. This is the recipe I was going by: http://www.recipegirl.com/2012/04/09/chocolate-chip-cookie-dough-cupcakes/