I have 2 Saitek throttle quadrants (not joysticks obviously but the principle is the same here)
I have them side by side on the desk. I set up my control settings on each by defining the control settings as LEFT or RIGHT as appropriate e.g. Cessna 414 LEFT (throttle) and Cessna 414 RIGHT (throttle). Doing it this way I can have different bindings on each throttle quadrant. However, both sets of bindings for LEFT and RIGHT show up on both quadrants.
It works for me but it is a very messy/clumsy method espcially as the bindings for the left throttle show up also when looking at bindings for the right throttle. There must be a better way of doing it but I have yet to discover it.