How to control different engine manufactures

Well, any older Atlas command engines will be TMCC, new ones may have PS/3.  In order to run PS/2, PS/3 stuff, you will need an MTH command system.  That's currently a bit of a conundrum, as there is no currently in production MTH command system.  MTH is promising in the future the WTIU, but I know of no concrete schedule for delivery.  The existing TIU & Remote set is available on the used market, but they're not cheap.

Adding TMCC or Legacy to a DCS layout typically involves connecting Lionel's signal wire to whatever wire is carrying power to the outer rails after passing through the Track Interface Unit (TIU). DCS sends its outbound signal via the center rail (red terminal) and receives communication back via the outside rails (black terminal).

So, adding DCS to a Legacy layout at its most basic level means connecting the TIU outputs such that the red terminal goes to the center rail and the black terminal to the outer rails, in whatever locations you're feeding a Legacy signal to (this assumes you have multiple power+signal feeds to electrically isolated segments of layout).

Since you already have power feeds to an existing layout setup for Legacy/TMCC, (and I'm assuming you want to keep things simple by not re-running existing power through the TIU) the minimum extra hardware would be a generic DC power supply going to the TIU auxiliary power input (barrel jack on the side of the box). This is known as "passive mode". In this mode you're just feeding a DCS signal into the layout, without the ability to perform an emergency power-off (emergency stop) via DCS, or control conventional locomotives with the TIU's ability to function like a Lionel track power controller.

You are correct that you won't be able to multiple-unit (lashup) locomotives from the two systems and run them with one controller (you can of course hitch a Legacy loco to a DCS loco and operate them using two different controllers, but that's awkward )

---PCJ