Before I start that, how thick is thr Arduino coating?
As in, how drastic is the change from Arduino to that AVR thing?
Jeremy,
this question is kind of an idiot test. If you have to ask it, you don't know enough to try it. If you now enough to do something like this, you don't have to ask that question because the answer would be obvious to you.
The fact that you asked the question gives you and all the rest of the world the answer, that you don't have enough clues about things to do what you think you need to do. Is everything lost for you? Not at all, you just need to learn to crawl and to walk before you can start thinking about running.
Best start here:
Figure out on your own, how for example PWM out works, what option you have, what pins can provide it and under what constraints you can modify that. When you do this, check the source code of the concerned Arduino functions.
Figure out on your own, what the boot-loader does exactly and what services it provides for application programs.
Figure out on your own where the source files are, how you can modify them and apply them. There's plenty documentation available for that.
In case you missed it, the common part of these tasks is the "Figure out on your own", where - in case you missed that again - the important part is "on your own" and not by posting questions on the forums. This will teach you a lot of useful things, most of them you probably don't even know yet that you need them and it will set you on track for you little project.
Korman