Hi AndiJay,
well, thats actually an secret, but after some searches you can find 'em for example in the subdir
arduino-1.5.2\hardware\arduino\sam\system\CMSIS\Device\ATMEL\sam3xa\include\instance
- there you can find all the predefined registers for each peripheral like
instance_pmc.h
But as far as i am concerned, i don't need to find em, 'cause all i need is the ATMEL datasheet.
All those registers or structures are named like the datasheet register names.
(Well one thing i had to search for, was the substructure for the timer counter sub-channels
which are accessed via TCn->TC_CHANNEL[ch].TC_REGNAME (Timer Counter n, sub channel ch).)
This way i got TC0-2, DACC, ADC, PWM, PMC and PIOA-D running (thats all i need so far).
Another thing i had to search for are the peripheral interrupts, which i now got running (for DMA),
but this is another story...
My way: learning by doing, because the documentation of the software is bad.
On the other side, the hardware is well described in the datasheet.