The reason they are digging holes, is because they are dust bathing in them. I have sand in my run because it drains VERY well. It's much cleaner than dirt and does not stick to your shoes (or their feathers) when it's wet. But as for the holes, they will just dig more. It's how they keep their feather clean and helps them to control ticks and fleas. I have sand in both my coop and my run. I wouldn't want anything else! It's so clean and easy to clean.What's the best thing to refill the holes with in the run?? More dirt, sand or sod?