I haven't taken the train, but did hire a guide in Salta to take us on a several day tour of some of the highlights in the region.

We overnighted in San Antonio de los Cobres (the terminus of the train) one night of our journey. S.A. is a pretty bleak place, but the scenery getting to and from there was pretty spectacular. My understanding is that the train is a very long day.

Depending on your timeframe and your budget, you might consider a private guide for a couple of day trip that includes some of the must-sees. This also allows you a lot more flexibility to stop, picnic, snap photos where you want.