The only VW I saw in Porsche Stuttgart was an early split beetle. On the other hand, the Wolfsburg factory museum has lots of different VW's as well as quite a few other cars that have been meaningful in the auto world.
Not far from the factory museum is another that is mostly VW and it is great. It is called the VW automuseum and this is their website
http://automuseum.volkswagen.de/ but they are not open every day so check first. You could spend a whole day in this museum.
You can check out the factory museum details on their website
http://www.autostadt.de/en/start/ as well.
We spent 3 days at the autostadt last time we were there and it is great.
Yogie