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I have a Thrusmaster FCS + TWCS 16000m and windows detects both devices (FCS + Throtlle). But once I'm in the game, only the FCS is active, and I have to use the "thruster button" on the front of the FCS to control thrust. I'd prefer to use the Throttle instead (which works perfectly in Elite Dangerous btw).

Did someone managed to make the throttle (TWCS) work with X-Wing Alliance ?
I don't think it's possible, If I remember well, each device is connected directly through USB to the computer. For the throttle (and the rudder if you have it) to work in that game, they have to be recognized as a single input device, which meant that the throttle would have to be connected to the joystick instead of to the computer, as XWA only work with one input device
If the software included with the stick does not have a function to "unify" the two devices, then I think your best bet is to use vJoy to create a virtual joystick that emulates a single device by mixing the axis of the two individual ones
You'll need to use the Thrustmaster TARGET software to set up a profile for the game which includes both controllers. When you activate the profile, it connects both physical devices into a single virtual device which will be seen by the game, and should allow you to use both stick and throttle together.
Thank you, It works nicely, I'm now able to use the throttle. I had to uninstall TARGET, install the drivers from the download area on the Thrustmaster website, the stock ones coming with windows were not working correctly. I mapped the throttle slider to the z-axis, disabled the slider on the FCS and that's it !