(And yes Blizzard validates both keys when you connect to Battle.net, so if you're going to try to use a fake WC3 key and your newly purchased TFT -- it will not work!)
If your key for WC3 is on your current installation, I'd really try to dig it out for the next time you need to install it (reformat etc).
as long as it is installed with the old cd-key it will be fine on battle.net, just never uninstall it unless you have your cd key again, or your screwed for battle.net after that.
Have fun with frozen throne if you get it, its my favorite RTS still.