I think the key is not "going cross-eyed" as much as it is relaxing your focus until the images merge. If you intentionally cross your eyes, it hurts. If you de-focus/relax your eyes until the images merge, it doesn't hurt.
That's more for traditional "magic eye" pattern stereograms where you want to relax your eyes to look off into the middle distance behind the subject instead of intensely focusing on something unnaturally close to your face.
