The receiver is fully connected to the Ardupilot with a spare channel to play with.
I've not used these bits, what exactly is the has a spare RC channel got to do with the Arduino hanging off the Ardupilot?
If it's just an RC channel I don't see how it's of any use for "talking" to the Arduino except in the most simple of ways. Certainly not for reprogramming. That said
Like I said I am a newbie to the Arduino platform so I am not sure what can and cannot be done. I do know that with only the Ardupilot that flight modes which are part of the programing can be changed via a switch on the transmitter which in turn change the flying characteristics of the quad. These modes are acrobatic, stabilized, loiter, simple. I believe that it is using PWM to do this. Also not sure how and or if this same method can be used to accomplish what I want to do but I believe it can. Something like if the PMW is in this range have the LEDs do this part of the program on the Arduino and if it is in a different range do this other part of the program on the Arduino.
I would like to somehow change how the LEDs are behaving
You don't have to "reprogram" the Arduino to do this, just write a program that accepts some data from the Ardupilot and drives the LEDs differently according to the data.
That should be possible using an RC channel. Do I have this right?
RC channel ---> Ardupilot ----> Arduino
If so what do you get into the Arduino? Pulse train, SPI data, something else?
I do understand that branching of some sort would be required on the Arduino and have no problem in doing that. I just need to understand how to communicate that from the Ardupilot. I am currently using SPI on the Uno to drive the addressable RGB LEDs and I am not familiar with what Pulse train or whatever the alternatives are if any. Separately the Ardupilot and the Uno function just fine by themselves. I just want to modify the program on the Uno to accept a signal from the Ardupilot to trigger a branch in the program on the Uno to make the LEDs behave differently. As it is now I can only start the Uno on the ground with the program I currently have. It is my goal to be able to change modes on the Uno in flight. Thanks for your help.