I understand how, but not the why

I am having an issue with programming my atmega328p in avr c. I have watched all the videos and I understand which bits to turn on, but what I don't get is how you know which ones to turn on and why. I get about timer1, 2, 0 and prescalers and ocra etc, but is there place that tells you which bits to turn on when you use timer1 as opposed to timer2 etc....I have seen no layout that I can follow and they just go to the next bit because they know which one to go to but don't explain why this...

I understand how, but not the why