What do you think is the best way to get from capital airport to beijing south railway station

Your time is a little rushing, and the traffic jam may make it worse, so I suggest you to take a taxi directly to the station and it may take CNY130-140 and 1 hour.
If you are not carrying many bags, you can also take Airport Express to Dongzhimen, then transfer to line 2, then transfer to line 4 at Xuanwumen, get off at South Station. It may take 1hour and CNY30.

I think subway is a better choice, since the traffic jam is so heavy in BJ.