Some of my free range hens are laying eggs all over, HELP!!!

Well...they are semi-free range. After our neighbor's dog got one of our hens I've been keeping the run gate closed, but it is just a fence with no top so some of my hens fly over the fence. I've thought about clipping their wings but if the moronic neighbor lets his dog loose again and my hens happen to be out, I want to make sure they stand a chance at getting away from it. I fell like clipping their wings would put them at a huge disadvantage against predators. We let them out to free range for a few hours in the evening when we can be out to keep an eye on them.
My problem is that 2 of the hens jump the fence and have been laying on a hay bail in the garage. So we moved the hay bail into their coop thinking they would lay on it in there, but one of them layed an egg today in the same corner of the garage where the hay WAS, and I don't know where the other one laid her egg. We also have 3 more EE's that we haven't knowingly gotten eggs from yet (they're all just starting to lay), I hope they aren't laying the eggs somewhere in the yard!! our 5 Isa Brown's lay their eggs in the boxes like good girls.
What's the best way to "train" them to lay in the boxes?? Should I keep them all shut up in the coop until the rebels get the hang of it? I would feel bad locking them up but I don't know what else to do.