Another way of doing this is to just use a mixer to mix your live OMSS sample replay and the MIDI device's output and then capture the whole lot.
I prefer the former since it gives me more options for post-production during the final mixdown. Sometimes, I record several components of a track in isolation, purely for this reason.
Yes, this was the best sound experience when I output the MIDI-keyboard sounds and Amiga samples through my yamaha mixer played the song back via OMSS and then I would adjust the volumes using the mixer. This worked fine and I got a decent rich sound from both.
I'm going to try save the the midi sounds as a MIDI file, and then import this onto a PC music tracker which can also playback Amiga .mod file and combine the two and see how this works.
As long as the playback routine is in sync I should be able record it as one file.
The GMmidi sounds on my PC don't sound as good as the one from Keyboard, but I'm sure I can find us an FM synth as a plugin and use this instead of sampled sounds for the MIDI.