I've only done it 1 way - batter in the cone and they came out great. Just whatever you do, don't overfill the cone 
I did it the other way. I place MM's in the bottom of the cone then stuffed with cupcakes I had baked separtately, added icing and done. My son had them prior to with MM's in the bottom and loved the special treat. Plus I was worried about the texture of the cone after the cupcakes had bake in them.
It is my understanding that it can be done either way. I think it is a preference thing.
It depends upon what you intend for the texture of your cone. The batter baked in the cone softens it a bit it to give almost a stale feel. Baking a cupcake and placing it in the top of the cone keeps the cone crisp.
I prefer to bake it right in the cone, and I fill it right to where the cup meets the cone (I hope that makes sense!) so that it just barely puffs out of the cone when it's finished. =]
I use the special pans that kupcake konz has, they're great! And they can be used for transporting them, too!
here's a link...
http://www.kupcakekonz.com/categories.php
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