I have to say that I have over 30 years of aquarium experience and have never had a problem adding rocks or sand with water in the tank. Actually, in most cases, I find it easier to add substrate with water in as gravity can be the enemy too. Thank you CML for the equation, greatly appreciated.
You have to use a bit of common sense when working with a water filled tank, this is true. For example, if you plan on adding 50 lbs of substrate to a tank, you can't simply dump it all in at one time. I add my desired amount a little at a time and certainly not from a great distance above the tank either. I submerge my container until it is just a few inches from the bottom and add slowly so I don't stress the seams or the bottom pane itself. If adding large rocks, you have to use even more care. When I added these, I painstakingly placed each one on the bottom by hand.
@Mac, I tried the big rocks, yes, they look great. However, I don't care how thorough I thought I was cleaning it, the gunk I found while removing it was alarming. Decaying bloodworms, parts of nightcrawlers, pellet debris, and other unmentionables were found. You may want to make sure your gaps are filled with sand to avoid this issue. Not to mention I'd love to see your set up when you're done!