yep, with most gear (well all gear ive used) you can assign the midi channel/channels they will use.
before using the computer sequencer, i used a very basic hardware sequencer (1midi in/ 1midi out) and a ran 4 synths from that all using the thru ports.
you asked "How do you determine which synth to control?" the only synth going into the midi in of the sequencer will be the controller (in a plain setup). as long as that synth has heaps of knobs it usually can do pretty much everything on all the gear.
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