Our girls lay in their nest boxes in the barn. Their nest boxes are on the floor so they are easy for them to get into. We also leave a wooden egg, like the ones for crafting, in each nest and most of the girls use the same 2 nests. We have also bred for and picked laying hens that lay at night or very early morning and who consistently lay in the nest boxes. We dont let them out till 7am this typically assures that all eggs have been laid in the appropriate place. Aside from when a new hen just starts laying we almost always  have clean eggs in the boxes. Some breeds will, "learn" to lay in a box, and SOME breeds, I think Runners are notorious for this, will lay anywhere, any time of day, in any conditions, with no regard for the cleanliness or safety of their eggs.
My advice, lock them up with some dummy eggs in a nest overnight or into the day if you have to and they will lay in the boxes. 
Oh and our Muscovy hens are NOTORIOUS for "holding it" until let out and then they RUN to their chosen hiding spot and lay a whole clutch. Silly ducks.