I've seen the cupcakes made in Starbucks coffee cups and such and was wondering if there was any special instructions that need to be followed or is everything the same for baking a regular cupcake?
As far as I am aware you can bake them in anything paper-ish...
If you are referring to Novacart cupcake paper pans, the temp should not go above 390 degrees. This is really the only thing you need to be mindful of when using paper baking pans, and the temp is different depending on the manufacturer.
Here's how Idreamofcakes made hers: