We have always picked up our Y.E.S. tickets at group sales. It's a window connected to the Disney Quest building, if I remember correctly, or very near that building. Almost at the very end of DTD, by Cirque, etc.
We do not do parks on every day of our trip, especially the first/travel day, so we pick up at DTD on travel day to be ready for parks on the next day. I believe that window closes earlier than guest services at the parks, maybe. If I recall, I had to pick up before 5pm there last time.
~Leigh (who is anxiously awaiting the January/February 2013 classes so I can really get started planning our next vacation - scheduled around Homeschool Days)