The chips programmed for an Arduino board do not have debugWire enabled. You'd need to enable that before you could use a debugger, which is going to interfere with the bootloader.
But you don't need to use the bootloader, since you upload using debugWire.
I've used ddd to debug Arduino code using a Dragon on both the m328 and the Tiny85.
It is a a mess to get setup but once up and going, it works pretty well.
It should be much easier with the 1.5 IDE since it allows you to alter
the build tools.