http://www.aamc.org/students/mcat/answerdocs.pdf
Go to the following link if you want to see a carbon copy of what exactly the answer documents look like.
Each booklet and each answer sheet are passed out prior to the start of each section. Once that section is done, they proctors will collect both the book and answer documents for each section, then go through each book one by one to make sure that people have not ripped out any pages. This is the reason why it takes longer on test day then at TPR or other places.
For the writing section, you will be given one answer booklet only, but you will not be given both prompts at once. Once the first prompt is done, they'll collect the booklet which has the prompt inside of it but you will keep your writing booklet. then they pass out the next writing prompt and when that one is over, they collect both the prompt booklet and the answer booklet.