I would set the MPU-401/AT to something other than the default I/O and IRQ settings so no program would attempt to use it unless I told it to in the install program. Then, if I wanted to use the GM/GS capabilities of the SCB-55, I would connect the midi out of the MCB-1 to the midi in of the MPU-401/AT. The midi should go directly to the daughterboard.
I have a similar setup, only I've not found it necessary to route from the MCB back to the SCB, as most games can be configured to use a different MIDI port address. (Those that I've played, anyhow)
Here's a mess:
Roland LAPC-I - Address: 330h, IRQ: 2(9)
MV PAS16 w/SCB-55 - Addresses: 220h, 320h, 388h, IRQs: 5, 7, 2(9)
IMFC - Address: 2A20h, IRQ: 3
Creative GameBlaster - Address: 240h
Since the two Roland synths are not used simultaneously, I've not run into any issues with IRQ sharing.
Here's a question, for anyone that knows - Why is it that in a Sierra RESOURCE.CFG file, you can specify different ports for several of the drivers (CMS.DRV, SNDBLAST.DRV, etc.), but cannot do the same for the GENMIDI.DRV? The MIDI address-changer utility works fine, but still...