I'm using Arduino 1.5.1r2 as well , the low level libs from Atmel are all there ,
though i do have to go grep'ing ever time i need a function ...
i did make myself a cheat sheet of locations when working on the PWM - they will be the same for adc :
.../arduino-1.5.1r2/hardware/arduino/sam/variants/arduino_due_x/variant.cpp
.../arduino-1.5.1r2/hardware/arduino/sam/variants/arduino_due_x/variant.h
.../arduino-1.5.1r2/hardware/arduino/sam/system/CMSIS/Device/ATMEL/sam3xa/include/component/component_pwm.h
.../arduino-1.5.1r2/hardware/arduino/sam/system/CMSIS/Device/ATMEL/sam3xa/include/instance/instance_pwm.h
.../arduino-1.5.1r2/hardware/arduino/sam/system/libsam/source/pwmc.c
.../arduino-1.5.1r2/hardware/arduino/sam/system/libsam/include/pwmc.h
.../arduino-1.5.1r2/hardware/arduino/sam/system/CMSIS/Device/ATMEL/sam3xa/include/sam3x8c.h