So, next question that I guess I never thought about; Does the egg box with the incubation medium have to have a lid? It's just for holding the humidity within the box, correct? I'm sure the incubators themselves are the greatest at holding humidity. Depends on your setup, but typically yes...what kind of setup are you going to use? If it's a traditional setup then use a lid. If you are going with the submersible aquarium pump type of setup you may be able to get away with not using a lid, but I haven't done a whole lot of research on that method...
So basically; if they all fit in the box, don't touch the lid (or sides for that matter), leave them in a clump. I'd say yes...you run the risk of tearing them if you try too hard to separate them...
As far as eggs going bad; I've been told/read that typically, bad eggs do NOT affect the good eggs, so just leave them alone. Bad eggs can affect good eggs. Although eggs that are healthy from the start don't typically go bad. If you candle them when they're laid and their are no veins, keep an eye on them as they will most likely go bad... If the bad eggs start molding, you really just leave them in attached to the others? It's best to get them out of there if possible. There are ways to stop or delay the molding though if it's towards the end of incubation...
Whew, just want to try to get all my ducks in a row before my first clutch comes. So many things popping up that I never really thought about until one of my girls actually ovulated!