Here's the
TSB for 99-02 model reprogramming, previous models may be similar. It can be done either with the scan tool, or one of two sequences described in the TSB using only the transmitter and key on cycles.
Looks like this is the pertinent one:
Program Method B (Customer Program Method)
1. Press [LOCK] button 5 times at 2 second intervals to resynchronize transmitter. Attempt to function transmitter, it working as designed discontinue programming.
2. Turn ignition to the run position (Allow Ignition chimes to stop).
3. Using original transmitter, press and hold the [UNLOCK] button on the transmitter for between 4 and 10 seconds.
4. Continue to hold the [UNLOCK[ button and press the [PANIC] button. A chime will sound to indicate that the transmitter programming mode has been entered (Allow 3 seconds for chime to sound).
5. Press a button on all transmitters to be programmed into the system including any previously programmed transmitters; a chime will sound when each transmitter has been programmed.
6. Turn the ignition to OFF position to exit the transmitter programming mode.
Seems to me that if you had another person do the same steps in the other vehicle at the same time, both would get sync'd up with the transmitter.
As far as how the transmitter works,
How Stuff Works has a good description.
Basically, when you hit the unlock button, the unlock code gets sent, but so does a security code. This code can be one of a few million numbers. If the code that gets sent doesn't match what the receiver in the car expects, it doesn't pay attention to the unlock code. When they match, it unlocks the doors, and uses a pseudo-random number generator (basically a mathematical formula that gives 'random' numbers in a certain sequence) to figure out what the next code should be. Your key fob transmitter changes this code to the next one with every push of a button.
Usually, there's a window of about 256 codes, so if you push the button a few times when out of range, it will still unlock the next time you try it. Hit it 257, though, and you'll have to resync it.
That's what the procedure above does. By putting the vehicle's receiver in program mode with the DRB or key cycles, it listens to the remote, figures out where in the sequence it is, and sets its own number generator there. Since it looks like these RKE systems are basically the same across Chrysler platforms of similar model years, I'd imagine that having both vehicles sync their receivers to the same transmitter at the same time would allow you to use one key fob for both. Only problem is, when you hit 'unlock', I'd imagine both vehciles would do so, if they were in range.
All this is just theory (the multi-vehicle part, anyway), and I doubt DC intended the system to be used like this. My truck had a Viper system when I bought it, so I can't try it out (and I don't have another DC vehicle to try on, either). Anyone feel adventurous?