Legoman,
FlightAxis Link data doesn't have anything to do with what vehicle is being flown. Only state data (where am I, how fast am I going, etc.) is transmitted. So, yes, your EA's should work with FlightAxis Link, just as they work for a human pilot. The Link can tell autopilot software what any aircraft is doing, and can send the autopilot's control data to that aircraft.
And yes, the FlightAxis Link can control the first 8 input channels. If you've mapped any of those to a vehicle channel above 8, that will still work. For instance, if you've mapped the knob (Input Channel 6) to a software radio channel 12, then it would still operate whenever the Link changed the value of it's Channel 6.