How do I create a clear object inside of another object (like say for instance the letter O which has a dark outer circle and a clear inner circle)?

To create the clear objects inside of another object, you will need to place the clear objects on a separate layer and then merge. This is called creating a composite gerber layer, and I have provided a movie tutorial showing how to perform this step:

http://www.screencast.com/users/Numerical/folders/Jing/media/62573854-822d-495f-a5cc-fbd75ecf5aa9