I was looking for this answer too, this sounded helpful!I have the clear, plastic Wal-Mart car mat flaps on my coop doors to keep out the flies in summer and it cuts down on cold drafts in winter.
I cut them to fit the inside dimensions of the pop hole so they swing both ways freely. Otherwise the chickens would have trouble pushing through if they were larger than the doorway and only pushed open from one direction. I cut them a few inches longer on top so they can be stapled to the inside wall.
It's never been any problem getting new chickens used to going through the flaps. All were able to master the flaps in no time.