bruuen-
Are you asking how you control which module you are playing at any given time? If so, that's a little more complicated question. Depending on your system and the devices in question, there might be several different ways to control which module sounds at any given time.
A MIDI stream has 16 possible channels. The simplest and most obvious method of controlling your modules is to assign one to say Channel One and the other to Channel Two. Depending on your keyboard, you might then be able to split or layer the keyboard in different ways, say assigning Channel One to the lower two octaves for bass and the upper three octaves to Channel Two for a lead sound. Some keyboards allowing you to switch using velocity or aftertouch (pressure applied to the key after the note has been played). Things get much more complicated when you switch your synths into "multi" (or combi or whatever the manufacturer calls it) mode. In this mode, devices can devide their synth engine into a number of different, independent units. This is what is meant when a synth is called "multi-timbral". What happens is that the polyphony of the synth (the number of simultaneous voices it can produce) is divided among the different modules (how this is handled varies). Normally, the different modules will respond to different MIDI channels. This would allow you to assign each different channel to a different voice to realize a full arrangement when playing back a sequence, for instance.
You can still use the different channel approach in this situation, but you'll be assigninig more than one per device then.
Like most of the really valuable information, hidden away in the back of the manual of any MIDI device, you should find a "MIDI Implementation" chart. This chart shows the MIDI information that particular device is capable of receiving and sending. Though there are many MIDI messages, not every device is able to utilize all of them.
I know this is very confusing at first (and even later on, for that matter). MIDI's uses have been expanded over the 20 plus years of its existence and they've found ways around some of its limitations. Believe me, it's a lot simpler than it was years ago when you had to learn to program things in hexadecimal (talk about confusing to us non-tech types!).
Ted