Train travel from Stuttgart to Madrid (Atocha)

I'm not sure which website you are referring to when you say, "i went into the site, it was confusing," but the best website to check European train schedules is the German rail site at www.bahn.de (switch to English at the top right.) If you click on "details for all," the major transfer points and the types of trains used will come up. However, Stuttgart to Madrid by train will take between 19 and 22 hours. All require you to head back into Paris, changing stations to Austerlitz, and catching the overnight train (EuroNight #409 or 477, or Night train 4053), transferring at either Valladolid (north of Madrid) or, on the longer runs, at Barcelona or Irun to local trains around 6:30 or 7:30 in the morning. But it's likely to be very expensive. You might want to consider a discount airline....Air Berlin flies that route via Mallorca, or take the train to Paris and fly from there....via easyjet or vueling.

Germanwings flies directly from Stuttgart to Madrid and has some very cheap fares.