What is the best way to debug a radio?
Assuming you have already built up your radio with components like what is shown on page 10 of your link, I would first debug and double check the circuit surrounding your radio.

Then I would find a sample piece of code or instruction set that can be used to turn some settings on/off. Maybe there is already a project out there using another radio in this Atmel family. You should be able to use your computer's serial port to send instructions to the radio directly. I would use a breadboard for this.

Basically, I would try to keep it simple as possible, and then add the complexity back in when I understand each piece thoroughly. Hope this helps!