Maybe you're right, I think I'll try to fully understand how the arduino code works and the I'll try manipulating registers and so.
Thanks for the advice.
I agree with Paul that you may not be ready to dig into the nitty-gritty yet. But if you want to try, I suggest this:
(1) Download the PDF manual for the Atmel 328P: http://www.atmel.com/Images/doc8271.pdf
(2) Download some source code that run directly on a 328P rather than using the Arduino IDE (see Sparkfun.com: multimeter kit, digital clock kit, etc...) and look at the code and techniques used there. Refer to the Atmel manual to see what the registers and each bit in a register is doing.
Keep at that until it all starts to make sense....
Digital multimeter source: http://www.sparkfun.com/datasheets/Kits/Multimeter%20Kit%20v15.zip
Digital clock source: http://dlnmh9ip6v2uc.cloudfront.net/datasheets/Kits/clockit-v11.zip
Even better, buy and build one of those kits, then MODIFY the source so you can see what happens.