Hi, Sam,
Welcome to the forum!
There is a notice on the RENFE/Cercanias web page. Since they are doing work at Recoletos, which is a station near Atocha, you will have to get off at Recoletos and take a free bus to Atocha. This will add a bit more time, so I hope you're not crunched. It will run every 6 minuteson week day rush hour, up to every twelve minutes at other times. The silver lining here is that they hope the repairs will be done by September 4, so you may not have to worry about this at all.
Here's the link if you read Spanish:
http://www.renfe.com/viajeros/cercanias/madrid/index.html