If you mean that you have 3 regular Pokemon caught, I think you should be ok, but I've only heard it from one person so I'm not going to promise it. It seems that the legendaries get generated before normal Pokemon, so the Tornadus should be in slot 1 for RNG purposes. Good luck.
I just caught Tornadus in the dream radar and am ready to pick it up. Unfortunately, I have slots 1, 2, and 3 occupied by other Pokemon. Has it been confirmed yet that the frames will jump up for each occupied slot before slot 7 (Tornadus) is obtained?