May as well use them up, but I don't know that putting down paper towels beneath them helps with the smell. It's worth a try as it doesn't hurt anything.
We've used the horse bedding in our coop for about 8 years and only change that every spring, but it was only this past year we tried them...
We use paper towels changed often the first 3-4 days, then horse bedding pellets. Those absorb the poop so no smell at all. We have two brooders in our living room and have no smells. There still is a little dust but it is reduced as the pellets let it sink in. We put a container of...