I am writing music for organ in LilyPond and listening to it via the LilyPond MIDI output through Qsynth/FluidSynth. I've been using Fluid_R3, but it only has a very generic (and not very convincing) "Church Organ" patch. I recently found JEUX, a soundfont with all sorts of organ stops, and I'd like to export a synthesis that works like a real organ, with multiple patches registered on each channel.
Is there a straightforward way to configure FluidSynth (or a similar software synth) to apply multiple patches on a single MIDI channel? If so, would I have to do something special in LilyPond for its MIDI output to work? (I could do something like multiple exports and add the sound files together, but that's a lot of complication!)