If you want to commute in Jakarta by using train, or you want to go the sattelite cities (Bogor, Depok, Tangerang, and Bekasi) from Jakarta, you can get yourself to the nearest railway station and decide which station you want to go. The train used to called commuter line. It is a train with AC (air conditioner) facility. But don't expect too much. At busy hours (before and after office hour) it'll be crowded until you can not feel the AC
Fortunately, compared with other transportation (like buses), the railway service has a guidance of train schedule, and also in every station now has several screens which shows the position of each train.
Another good thing is some railway station are closed to TransJakarta shelter so it might help you to continue your trip. The railway station are:

• Cawang
  
• Manggarai
  
• Juanda
  
• Gambir
  
• Sudirman
  
• Kota
  

If you watch the map carefully, you'll see that in some destinantion, you need to transit to a particular station, such as Manggarai.
For example, you are from Depok and heading to Bekasi. You need to take the train from Depok which heads to Jakarta Kota or Tanah Abang. Get off at Manggarai station to get the train which heads to Bekasi.

Another info:
Sometimes people fall asleep during the trip that lead him to past the destined station. Don't worry. As long as you are in the station and not make a card tap in the exit gate, you can still go back to your destined station by taking the train with reverse direction.

Hopefully, this brief information is useful.
If you're still confused, do not hesitate to ask.
There is a saying in Indonesian, "malu bertanya sesat di jalan" (If you embarassed to ask, you might get lost)
And the saying get a continuance made by the young people, it goes like this.
"Malu bertanya, sesat di jalan. Kebanyakan nanya, memalukan." (If you embarassed to ask, you might get lost. Too much asking, it's embarassing)