Matt asks a good question. If you join a club or operate with others on a regular basis, it makes sense to use the same control system everyone else is using.
I'm not sure about Atlas. Some, or maybe all MTH locos with Protosound 3.0 (PS3) can be run under Digital Command Control (DCC). This is the system 2-rail modelers in all scales, including O, have been using for over 20 years. It's supported by multiple vendors. In other words, unlike DCS or TMCC / Legacy, it's not proprietary to a loco manufacturer like MTH or Lionel. I don't believe that DCC is much more expensive, or more difficult to install than DCS. North Coast Engineering (NCE) is one popular DCC supplier that has a nice, fully featured hand-held remote. The time to decide about DCC is NOW, before you acquire too many locos to convert over!
The last option, a "nuclear option", would be to strip out all of the OEM electronics and install one of the direct R/C systems. A couple that have been mentioned on the Forum are AirWire, and especially Ring Engineering's RailPro. These systems send a radio signal from a physical hand-held controller directly to the loco. They don't need any kind of "command base." They are typically designed to modulate power to the motor(s) from an on-board battery, which is sometimes known as "dead rail." However, the radio receiver ("decoder") in the loco doesn't know nor care whether the input voltage comes from a battery or from the track. (If there's AC on the track, it would have to be rectified and smoothed by a capacitor.) If you go with one of the direct R/C systems, YOU will be able to control your loco at a local club or train show, no matter which system(s) the club is already using, but the other club members would have no way of taking control of it, for better or worse.
Obviously there are a lot of factors to consider and it's a personal decision. Both OEM systems have suffered adverse developments in supply the last couple of years. Neither one makes a physical hand held right now, and I don't personally like running trains with a cell phone. If I had the ability to choose over again, I probably would have gone with DCC or direct R/C. My $.02.