For a list of config files in your system:
You are gonna have to get to know your hardware. Gonna have to learn the operating system, including the kernel. You are gonna want to keep the system lean and built to your hardware. That is where the USE flag come in handy in your make.conf and by using the package.* files.
Optimizing is the beauty of Gentoo, but you need to learn how it all works.
Some great info over at gentoo.org
It's just taking the time to read it.