For a single card solution and using a mixer, to hear the MIDI music only from the MKII AND the Sound Blaster digital fx sounds, go to the volume panel in the SB's software mixer and turn the MIDI channel's volume all the way down to 0.
Since the MKII unit is independent from the software control of the Sound Blaster's software mixer, you can still hear the MKII, since the MIDI signals from the Joystick port still goes to the Sound Canvas unit, and the sounds are produced and sent to the mixer instead.
Instead of using a mixer, you can also route the output from the MKII back to the LINE-IN of your sound card.
I'm using the above mixer with one of my desktop systems, with inputs from the PC, MT-32 and the SC MKII.
For individual MIDI port assignment, going dual sound cards (with or without the now-difficult -to-get MIDI card) is a better solution.