I am trying to get my 9 cap to give me a little down elevator when the flaps go down and I just cannot seem to get it to work, can someone help me set this up.

If you have the ability to separate your trims and have flight conditions you can make you your flap switch your condition switch then when you deploy the flaps you can re trim the elevator.

Can you do it without the flight conditions switch? just so the elevator retrims itself when the flaps are down?

Sure just set up a program mix. Master is flaps, slave is Elevator. You can use a rotary knob as a rate control so you can dial in more elevator throw or reduce it.

Ok, so that's sort of working, only when I adjust the rate on the transmitter for the stab position, the flaps are up and the elevator can't be trimmed out, but on the middle position and down position where I need to be able to trim it, I can't do anything with it. I tried the different switch positions and none of them allow me to change the rate when the flaps are down, I hope that makes sense. Any ideas?

Go to the Futaba website and look up your transmitter, then look under frequently asked questions for programming your radio, it will show you how to do what you want step by step. I used this for my 8cap programming.