I'm currently using an Atlas Commander DCC system on my N scale layout. I chose it because as a beginner, I built my track plan based on one in an Atlas book (I believe it was this one), and I was very low on cash. ;)
I've been very happy with the system, but I do know it has some limitations. I'd love to switch to a Digitrax Zephyr system at some point, as I've heard nothing but stellar feedback on that one...but will I have to rewire my track or otherwise tear up my layout in order to do so?
Nope, if your layout is running well now, all you need to do is disconnect the two wires from the layout to your Atlas unit, and attach them to the Zephyr.