According to Dr. Bob Purcell, threads that are "stacked" on a spool should unwind from the side of the spool to avoid twisting.
Think of a roll of toilet tissue paper. When you pull it off the cardboard tube from the side, like when it's mounted on a tissue holder, the paper comes off straight and flat.
If you pull it off the side of the toll, like when it's just sitting on the counter or vanity top, the paper will be severely twisted. Same thing with the thread.
Threads that are "cross-wound" (like most large cones for long-arm machines) should unwind from the top of the cone, and work well with a weighted cone holder with a thread guide directly over the cone.
You might find more helpful info on his troubleshooting chart:
http://www.superiorthreads.com/media/docs/Troubleshooting_Guide.pdf