Use a regular titanium drill bit, you can epoxy the rock to the rod for a more stable stack also, attaching the rod to a acrylic base is also and option if it is a new tank setup. I tried several masonary bits with no luck, but with the titanium bit it goes into the rock like it is cheese.
I talked to Richard at Tampa Bay Saltwater the first time I did it and he said if you have any sponges that they will more than likely die after 5 minutes and anything over 15 minutes, and die of will increase on other livestock.
Tape off an area the size of the base of your aquarium on a plastic drop cloth and pull the rock that you think that you want to stack and drill away, if you drill in the wrong place, just drill again untill you get the stack you want. If it starts taking to much time put the rock back in the aquarium or a container with some of your water change water.
Hope that helps!