Hi vortix2950,
You seem to have two projects on the go here, both a transmitter/receiver system and a quadcopter flight controller.
Building your own quadcopter flight controller is a great project, but it's also quite a difficult challenge and takes time, we're talking months of development. It's a project in which the amount of code or sketch size is actually relatively small, but it's the concepts that take a while to understand.
As I mentioned, you need to break the system down into smaller more manageable tasks, while maintaining a clear idea of what information is passed between them.
Before you proceed, I feel that you need to answer the questions you pose regarding the pilot input. Sometimes it's worth stepping back and reassessing the situation. Might it not be easier to use an existing transmitter/receiver system?