Oooo....Ahhhhh..... 
You win. That hacking page seems a little out there. I tried looking at some of the user code for stuff and I know how to setup the registers and code and all that blah blah blah. I just need something that says hey, this is what the "correct" way is and this is the "arduino" way. Not to bash the arduino, but having those routines seem to mess some stuff up for people used to plain barebones coding style. I just can't find anything that says like where the preprocessor directives would go, or like what the best thing to go in the setup() is. Because looking at user code, they declare and define variables before the setup() and then declare and define variables within the set up. Is anything before setup() still a procedural flow?
I did see something about the loop function about making it loop or run once. Thats nice and easy. What are the functions that are to be used for interrupts? For example when a interrupt is triggered what is the function name for the ISR?
Lemme know if you don't understand anything, I just have so many questions to have answered before I order one. I already have 2 stk500s but you can't mount those on a robot! >_<
-John