It's really quite easy to do dual aileron servos with the RD 6000 ( I use one with my Ultrastick).

Put both Aileron servos in the wing so that the outout shaft is closest to the leading edge of the wing.

Put the control rods on the outboard sides of the servos. That is, closest to the wing tips...

Plug a short extension into receiver channel 2. Mark/label it "R" for right. Plug another into channel 6. Mark this one "L".

Go into the "etc" menu and activate flaperons.

If you DO NOT wish to use the ailerons as flaps as well, go into the PF menu and set the flap endpoints to zero. This will in effect inactivate the flap switch.

Label the servo leads coming out of the wing L and R. Plug them into the extensions coming out of the reciever... L to L, R to R

Switch everything on and centre/adjust the ailerons mechanically.

With the wing in position, stand behind the airplane and visually confirm that the ailerons move the correct way when you wiggle the stick.

You should be all set to set up expo and D/R !

FWIW, I use different coloured cable ties on my servo hookups... Red=Left=Port, Green=Right=Starboard... I then match green to green, red to red when hooking things up.

I've also forced myself to stand behind the airplane before each flight and visually confirm that each control surface moves the way it should before starting the engine. I've manged to catch a missed connection a couple of times and probably saved myself an airplane.