I have both DCS and Legacy on my pretty large layout, and run both Lionel and MTH trains. 99% of the time I use DCS.....IMO it's a much better system. So Atlas and DCS will be a great combination.
I assume that you have a Lionel Legacy Command and Control set... In what ways do you find DCS superior? Ease of set up? Reliability? features? Are there features that DCS has that Legacy doesn't have? I'm not trying to play "stump the chump" here. I have not used DCS.
I would say that going through the MTH ScaleTrax catalog I was startled to read the following in the FAQ section of the MTH catalog:
"Question: Does the blackening of the center rail need to be removed for DCS operation?
ANSWER: Yes, I found that if you don't remove the blackening on the very top of the rail you get sparking from pick up rollers in conventional or DCS operation."
Now, I could see a disclaimer from MTH that says: "If you use DCS and use BRAND X's track you will need to do this to BRAND X's track before you use DCS." Instead, MTH is saying that "before you use our operating system on our track, you have to make a significant modification to our track before you use our command system on it." I would think that your company's premier track system should be ready to support your premier command system right out of the box. I can't imagine removing the blackening from the top of the central rail of all the track of a large layout. Are there other modifications that need to be made to a layout in order to run DCS?