the thread is the last seam you sewed. should be on top when you fold the four patch in order to clip the thread.
this link just shows how to sew the seam well
http://quiltcetera.wordpress.com/201...-a-four-patch/
this shows the seam four patch done-http://quiltville.blogspot.com/2005/06/spin-those-four-patch-seams.html
better photos-http://www.american-quilting.com/blog/?p=698