There's an article about it in the latest issue of Autospeed, a weekly web publication ($34.26 for 50 Issues), so you have to pay to read the full article, but I find it a good magazine worth the subscription.
The building is mostly glass, the floors ar wooden, and the cars are individually hand assembled.
The bins that you see in the pictures are automated, moving to different stations around the car, guided by magnetic sensors under the floor. The factory is located in Dresden, Germany, though the article doesn't state if you have to be purchasing a Phaeton to take a tour. Let's hope not.