I would assume there's no problem keeping CDs/DVDs in those, as someone recommended to me once that I store them in a DVD wallet/binder. The only other thing to remember is to keep them in a cool, dark place, out of direct sunlight and away from huge extremes in temperature and humidity. Generally storage inside a house (that's usually climate controlled anyway) is fine. As for stacking or laying the wallets/binders flat, so long as nothing heavy is on top of them, I don't see what putting them on their side or flat would be a problem. The other alternative is using slim jewel cases; while those are stackable, they also slide around if you try to handle many at one time. Anyway, I see no problem with how you're storing them.