As you are going to mess with the ASF, prepare to meet Atmel's hell.- I speak from my own experience. Too much junk code! It's like the Amazon rainforest. It's very easy to get lost in it. So far I have ported a couple of libraries from ASF to Due. A much better start to understand the SAM core is to get familiar with the Arduino libsam library.
There you will find the source and include SAM drivers like ADC, PIO, PMC, RTC, TWI, etc. The duo Arduino-Atmel did a great job in it that deserves the benefit of a close look. Good luck!