Homemade nestboxes are OK if they're well made. The biggest problem seems to be the doorway - lots of people put it too low and then have problems with the babies falling out before they're ready to fledge and getting hurt. Our nestbox article at
http://www.littlefeatheredbuddies.com/i ... boxes.html talks about the characteristics of a good nestbox.
Wood shavings make better nest bedding than paper towels do. It's fairly cheap, and you can find it in the small animal (rodent) section of most pet stores. Aspen and pine are fine, but you need to avoid cedar because it's too aromatic for birds. Kaytee is a good brand, it's nice and clean. Some brands have a lot of dust in them which is not good for the babies.
Have the parent birds started incubating the eggs yet? Some pairs will start sitting right away and others will wait until several eggs have been laid. You can move the eggs into a different nest, but if the parents have already started incubating it's important to make sure they move into the new nest quickly, like within half an hour. Eggs can sit around at room temperature for a week or more if incubation hasn't started. But when incubation begins the embryo starts growing, and if the egg gets chilled the embryo will die. Many parent birds will accept a new nest very quickly but some won't, and if your birds don't like the new nest you'll need to put the eggs back where they were.