Now, submarines aren't new to the World of Warcraft. The gnomes used them in the second war, and you can build them as a sea-faring battle unit in Warcraft II. In more recent uses, there is a makeshift goblin "submarine" in Venture Bay that is essentially a space rocket on its side, though I'd imagine the new submarines will look a bit less slapdash.
As to where exactly the subs will go, it wasn't said, but I'm banking on the Abyssal Maw area, or similar areas thereabouts. Zeppelins and ships already have most of Azeroth covered, so it's likely we'll be seeing a few new islands in Cataclysm as docking points for our awesome new subs.
World of Warcraft: Cataclysm will destroy Azeroth as we know it. Nothing will be the same. In WoW.com's Guide to Cataclysm you can find out everything you need to know about WoW's third expansion. From Goblins and Worgens to Mastery and Guild changes, it's all there for your cataclysmic enjoyment.