Get a hardware debugger for atmel to use with your Due. AVROne is the current one. I bought a JTAGICE3 a ways back after the price drops and just got it working with an UNO and boy is it nice to get back to source debugging and hardware breakpoints. debugWIRE is plenty fast for upload and control. I debugged a port of some IR Receive interrupt driven code in minutes. I have a blog entry coming on setting it up. If you are building under AS you hare 1/2 way there.
Other choices in almost free hardware debugging where you get the hardware debug support with the development board have proliferated for a while. Just setup an STM8S Discovery and its great. Other great options are the TI selections, and ARMS, etc.