Please explain what steps you've taken to try to get it to work with your MT-32. Then we can figure out what else you need to do. Also, are you using DosBox or ScummVM to run your game (which one are you using)?
My immediate guess is that you didn't run the SQ3 installer & choose the MT-32 as your musical device. Or you'll have to edit the Resource.cfg file and make sure it's using the MT32.DRV for your sound driver
I'm using DosBox and tried several settings for the midi side.
Also put Audio in config on MT32.drv but no effect i'm affraid. Music sounds terrible.