Connecting FlySky FS-T6 to ArduPilot (mission planner)

Please bear with me, this is my first time making a drone and using a transmitter.
I have got a FlySky FS-T6 transmitter that I have finished configuring and connecting to its receiver.
I connected the receiver to a PPM Encoder and connected that to my Pixhawk’s RC IN
and connected the Pixhawk to my laptop, everything is connected correctly but I still can’t control my quad copter’s motors with my transmitter.
I am not sure of what settings I should change or alter in Mission Planner, nothing works.
Is there anything additional that I have to download?
What should I do to ensure that everything is connected and working?
and is there a step-by-step guide on how to connect my transmitter to ArduPilot:Mission Planner from A to Z? including motor tests and whatnot.
Thank you for your help in advance.

http://ardupilot.org/copter/docs/initial-setup.html