You can encourage laying in the nest boxes in a couple of ways. First do you know what time of day they are laying them? Usually hens lay in the mornings but mine are mostly noon/early afternoon layers. If you know what time of day they lay, you can try to lock them up in the coop during this time to encourage laying in the boxes. Another trick is to put golf balls into the nest boxes to encourage laying there. They will all want to lay where the others laid -so I would also put any eggs found on the ground into a nest box immediately so the others will follow.
Egg color: the color can fade slightly over their laying period-both for the season and as they get older. What I mean is: After a break over the winter, I have noticed the egg color is darker, as the spring/summer goes on, the eggs will get lighter/less pigmentation. Also, your older hens eggs will be lighter than when they first started laying. I have a 4 yr old Orpington and her eggs are a lot lighter than when she first started laying. (Size will also get bigger as they get older)