What is the best way to get from the Chamartin train station (arriving from Paris at 0900 hrs) to the Atocha train station (leaving for Malaga at 0930 hrs) and how long will it take? Do I have enough time or should I take the 1230 hrs train instead?

I haven't actually done it, but recently used Atocha station a couple of times. Some trains stop at both stations - any chance of that?

If not, and you won't have much luggage, you could take the Metro - Line 10 to Tribunal, transfer to Line 1, which will take you to Atocha. Map here: http://www.metropla.net/eu/mad/madrid.htm

I'd probably opt for a cab; they are cheap and much easier. Either way, I think half an hour is very tight. You *might* make it, but I wouldn't plan on it.

I would not plan on making this connection because of several reasons. If you happen to be arriving on the overnight from Paris (?????) that train, or whatever train you are arriving on could very well arrive late. If it is #408/9 the hotel train from Paris it does NOT stop at Atocha. Last year we overnighted from Paris and the train was a good 1/2 hour late into Chamartin but we were ending our trip in Madrid so didn't worry about it. I would most definitely take a cab to Atocha..the Madrid Metro is very good but you don't want the hassle with the luggage on the Metro and at that hour of the morning the Metro will be busy.
I would strongly advise you to plan on taking a later train out of Madrid that way you don't have to worry and probably could easily do the Metro thing.

13 minutes by local train (cercania) thru the tunnel from Chamartin to Atocha. There are departures from Chamartin 9:03, 9:08 and 9:10. Timetable on http://horarios.renfe.es/cer/hjcer20...LEO=10&I=I

Yes, the 409 overnight from Paris to Madrid. Very good input from all "THANKS" - I think you are right, the train will most likely run late so planning on the later one to Malaga is probably a good idea.

Keep in mind also that it's going to take you some time to get to the Taxi stand from the Train platform: allow about 10-minutes for that exercise but it could take longer if you are in a carriage far down the train.