How can I find the low-level registers of the Due in the Arduino IDE? Any header files for the Due to change its clocking?
Read the datasheet / programming manuals for the chip. The Arduino Due is arranged to run at 84MHz.
I cannot find the "sam" library in the Arduino IDE. Only avr is present. How can I find this sam library?
Install it. The IDE is (fairly) modular these days.
But I have to ask... why do you want to run at 16MHz?