I would first try a single gameport setup with the AWE64. If that works, it will keep things simple. But since your HOTAS system (Flight Control System + Throttle Quadrant System + rudder pedals) is old stuff with lots of extra features, there are some chances of hitting the MIDI IN/OUT issue when using it along with the Sound Canvas. If so, I would connect the Sound Canvas to the sound card, and the HOTAS system to the I/O card. The former card is guaranteed to have a gameport with MIDI IN/OUT, while the latter card should have a standard gameport with +5V/GND if needed.
I have attached some files for a Thrustmaster FLCS + TQS + Elite DOS setup. You will find more info, drivers, patches and utilities for Windows 9x here: http://www.stickworks.com/