That’s the way I started but eventually used two FlightSticks. Banking movement with one hand (forward, backward, sideways), rotating around two axis with the other (barrel roll, pitch), and the thumb sticks I used for up/down and left/right. Although I might misremember some details. There was a time when I really wanted to add a pair of pedals, too. Ah, to have that much time to spare again.
The Macintosh version of the FlightStick had an ADB (Apple Desktop Bus) plug that had a port on the other end so you could plug in another device. It’s been 30 years. Do you think I might misremember? Maybe it was a FlightStick and a Saitek joystick? If you are running the original game on period hardware and tell me that the software wouldn’t know how to tell two different joysticks apart regardless of which type, then I guess I’d have to admit that there’s something fishy with my memory.
look into "period hardware" which is itself a "dual joystick" (typically literally sold for use in descent). it's a gimmick that sold i.e. why have one joystick when you can have two. Then you should just have a single i/o interface to your MIDI game port.
I dug around in my archives and found this post, someone is running Descent in DOSBox on an XP machine and using two USB joysticks and xpadder to set it up.
THE way to play Descent was with a Spaceball Avenger. I was a beta tester for one, holding it in your hand was like your brain interfacing directly with the ship. Sadly the sensors broke over the years and I'm settling for joysticks.
The wingman was amazing. Lot's of leeway and light and smooth. It seemed to have been built for environments like descent, where your fighter swooshed gracefully through space under any 3d angle.