I have questions and comments but most likely not any answers.
So, I created two multi-instruments pointing to the same hardware module, an Integra-7 (I-7). These multis appear in the library and I can assign either of them to MIDI tracks. MIDI notes will playback when using either multi. Is this not occurring on your end? Note: I've not attempted to setup sounds banks for the I-7.
Does your external synth come with a software editor provided by the manufacturer or a third party? If so, then the sane thing to do is to use the editor. Saying this based on using the Yamaha MOTIF Rack XS at one point, and currently the I-7.