I know nothing about these MTH units except what I just got done researching on a google search. Apparently they are made to run one PS2 or PS3 locomotive and be able to access the most popular functions of the loco.
A couple of key items I learned: For one, no programming of the loco is required. Simply set the loco and cars on the track, power up the transformer, turn on the remote, and you're ready to go. One caveat though, make sure that the loco is set to factory defaults, or it will not respond to the remote.
The other key item: the remote must be aimed at the receiver in order for it to work, much like aiming your TV remote at the TV in order for it to work. If your aim is off a little, it still usually works fine, but too far off, and the receiver fails to pick up the signal.
With these two key points in mind, I'm kinda' thinking you might be able to do this.............. Keep your two receivers as far apart as possible. One for one track loop, and the other on your other track loop. Then, if the two receivers share the same frequency (or infrared signal, or whatever they respond to), you should be able to control both receivers with one remote! Just point your remote at whichever receiver (and thus train) that you wish to control, and have at it. One remote? That might be pretty handy!
And if each remote only works with its matching receiver, that's not a big deal either. You should still have independent control of you trains, just each with its own remote. In this case, you probably wouldn't have to be worried about how far apart the receivers are, although there could be some unwanted interference if they are too close together.
Give it a try and see what happens. You can trust in me, 'cuz since I'm far from the sharpest tack on the electronic bulletin board, I'm NEVER afraid to experiment with other people's trains!
