Each IR receiver has 2 outputs (red and blue), which are controlled by the corresponding color wheel on the remote. This would be for control of different elements on the same train. However, each IR receiver and remote also has 4 channels, controlled by a switch, so you can set each train to a different channel on its respective receivers, and then change channels on the remote to control different trains.
I've bought it both ways, but I don't think they include the more expensive rechargeable battery boxes when you get them in the kit.
And my personal preference is for the yellow cargo train, and the new blue one coming out this summer.