Starting with the MTH DCS Commander

Any locomotive you want to use must be in "factory reset" condition, which can only be done with the full DCS.  If they're brand new and never run on a DCS system, they should be ready.

Red terminal goes to the center rail.  Also, you don't have to run the power through the DCS Remote Commander, you can run it right to the track and just run the DCS-RC in passive mode by just connecting it to the track, it'll be powered from the track connection.

Tips?  Point the remote at the base, they're IR coupled.

Indeed.  If your two tracks are in the same room you might be able to independently control each track using a single remote by aiming the remote at the 50-1033 base unit you want to control.  IR will bounce off walls, so you can put little cardboard (or whatever) shield around that little red lens on the base to receive IR beam from specific directions.  Within reason you can extend the length of the cable from the base unit to your track beyond the standard red/black banana cable length.  This might make is easier to position the base units for independent control of the two tracks taking advantage of the directionality of IR beams.

I'm not sure this will be all that easy to do, depending on the room,  The DCS RC was really designed as a true "starter" system, and if you want more than a single locomotive controlled using DCS, it's probably time to upgrade to the full DCS system.

Actually, as long as they are well adjusted, they can run together, they will both do they same exact thing when you invoke a command from the remote.

This will inevitably lead to one of them stopping in the middle of the track somewhere while the other swaps passengers at a station.

As long as you are good with that, no biggie.

Start them widely spaced on the layout and if they creep together, move one away when it gets too close.

The OP says he has two physically and electrically isolated layouts.  As he asked for tips, I'm merely suggesting he might be able to independently control both layouts with a single remote by managing the placement/orientation of the base units.  The "tip" is to observe that the handheld IR remote is directional while the base unit is omnidirectional...but the base unit can be altered to become more directional. 

This would be difficult to do with RF remote systems.

I'd sell the two DCS RC units and put the money toward a real DCS system.