http://www.sheldonbrown.com/frame-spacing.html

http://bikeforums.net/showthread.php?t=260417

Check these two above links. These will help. They helped me greatly with exactly the same situation you have. The first, from Sheldon Brown, is mainly for frame spreading, but the bending and measuring techniques are applicable for aligning the rear triangle.

The second link is in reference to a bike that I had the same trouble with. Ended up the rear triangle was not in line with the front triangle, and the fork legs were bent to the side. I used the advice from both pages to get the frame in the thread in good shape, and have since fixed a couple more that weren't tracking correctly.