Foldedbird, what a fun pattern! I think I'll add that to my pattern pages!
The instructions are just to take one of the 4 rectangles you've made, and fold it in half, so it's wrapped around one side of the plastic part of the flip flop that goes over your foot. Then you just sew it closed, so it's attached and is completely covering and around that plastic part. You do the same with another rectangle, to cover the other side. Then repeat for the other flip flop.
Hope that helps. Thanks for the pattern link!