I got rid of the neck and shoulder fatigue problem by quilting standing up. I place my machine on my cutting table. It is even better now that I have a styrofoam table surround for this setup -- creates a nice flat area. However, I still think the biggest help is standing up. My shoulders stay low and relaxed that way.
Here are links to the instructions for creating a styrofoam table surround:
http://www.youtube.com/watch?v=g14go...ure=plpp_video
http://www.youtube.com/watch?v=yAS25...ure=plpp_video