If I was doing it (I haven't before) I'd probably try the first time with both batters. Put some cupcake batter in, a spoonful of the browie batter, then more cupcake batter on top.
Wasn't something like this featured on CakeSpy?
Theresa 
I'm thinking if you put the cupcake batter in first and then a drop of the brownie mix on top, the brownie will sink to the middle as it bakes because its heavier than the cupcake batter.
This makes me want to try that now!
If it doesn't work out to bake at the same time could you just bake the cupcakes and brownies separately and then use an apple corer to core out the middle of the cupcake and use the corer to cut out a perfect sized "middle filler" of brownie for the cupcake?
LoL - did that make sense?
I like LogansMommie's idea.
And I thought of using already baked brownie--make a real fudgie one and use a scoop--but the cake batter has to be cold or real thick or something. And I don't think plopping it during the baking is a good idea. I could be wrong but I would not try that.
Apple corer I think is brilliant. Lotta work but brilliant.
Y'know what's another idea? A nice big dollop of ganache inserted right as it comes out of the oven. Take off the top plop 'er in and replace. mmmm
But I am not a cupcake guru.
I have made cupcakes with cookie dough in them. I put a small scoop of batter in the liner then added a ball of cookie dough in the center. I added more batter to cover the dough. Baked like any other cupcake but a yummy surprise in the middle!
I would bake the brownies first and cut them into bites. Then a spoonful of cake batter, brownie bite in each one, and fill with the rest of the batter. It will obviously take a little less time to bake since the "center" is already done.
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