Well, almost everything has been said, but I can always find more to say.
I would never take the metro from the airport to Atocha, especially now that the Cercanias (commuter line C-1) goes directly there from T-4 and the airport express bus also takes you there with very few stops. You have to change several times on the metro, and there are lots of pickpockets in prime travel time.
The Cercanias train is faster than the airport express bus, but it runs less frequently, only at 28 and 58 past the hour, and it only stops in Terminal 4, which is used by Iberia and its One World Partners (American and BA are probably the most familiar). So if you land in T 1-3, you will have to take an intra-airport bus over to T-4.
The Airport Express bus stops at all terminals and runs every 15-20 minutes. So depending on timing and where you arrive, it might be the easiest way to get to Atocha. Some info here:
http://madridman.com/blog-madrid/2012/01/madrid-airport-express-shuttle-bus/