Adam pretty much covered it, though he does a bit more then I typically do. Most people will tell you not to worry about it because the good egg will be protected by the immune system of the embryo. And usually thats true, however I have seen good eggs go bad because they were attached to rotting eggs so if I can do it safely, I always remove the bad egg. Usually it'll peal away fairly easy if the rotten egg is sweating, if not I'll open and empty the rotten egg and then trim away as much of the shell as possible. If there are windows on the good eggs they'll usually be fine, but if you want you can touch them up with some liquid bandaid (which now comes in a package of handy applicator swabs) Sounds like you pretty much got it covered already.

Mark