As far as the dumping out the hay, I always put hay in the box first. Most of my does will pull it out, but since I put the boxes in 5-7 days before I expect them to kindle, I am not worried. after that, I give them their normal hay at the morning feeding, I find that they prefer to put it in themselves. They will eat it until they start feeling like making a nest. When you see them gathering it (making bones, so to speak) then put extra in. They will stop eating it and start making a nest. Sometimes they will make a nest one day and tear it all out (or eat it) the next, only to make it again the next day. With new (first-time) does, if they haven't made a nest by the 31st day, I start putting it back in the nest box again, because sometimes they don't get the instinct to make a nest the first time.
I don't have trouble with any of my does using the nest box for a "potty" corner, so putting the nest boxes in early is not a problem. With a first-time doe, it is more of a problem in the winter (or when one is working away during the day) because if they don't make the nest or pull fur, the kits will be in trouble. I give first-time does a lot of slack. Nest building, fur pulling, and nursing instincts don' always kick in as well as they should. Still, I find most new rabbits have no trouble at all. Highly intra-bred varieties of rabbit have more trouble than cross bred rabbits. That means that meat crosses like mine (not so devastating to have a problem) are less likely to have a problem than highly line-bred show rabbits. Trouble is, losing "expensive" rabbits is a lot harder to deal with.