The device and unit information might be in the DOSDriver itself (a plain text file), not the icon information. But note the naming conventions of the DOSDrivers - Fx0 is for unit 0, Fx1 is for unit 1, etc. (where x = A, B, or C). You shouldn't need to edit them, just have the correct one(s) enabled. I think the default install only puts Fx0 into Devs:DOSDrivers and the rest are in Storage. So if your devices are set to 3, then they won't show up by default.
And I think FlyerInit needs to run from user-startup, although I don't recall the exact arguments.
What version of the Flyer software are you using?
Been a while since I set up my Flyer, I may not have all this right

And FYI, Amiga-to-Flyer transfers (i.e., DH1 to Fx0) and vice versa are absurdly slow. Within the Toaster interface, Flyer to Flyer is fine.