Gentoo Optimizations Benchmarked (Linux Magazine)

Gentoo installs patched packages from its own "ebuild" information.
If you upgrade, it will drop your previous package and install a new one.
You can modify this behaviour in multiple ways, of course.

You can manually interfere within the unpack and compile process to add some patches, but they will go away next time you build the package.

If you want to change a package on your own, you have to copy its ebuild file and add your patches/modifications there. you may want to create your own "overlay" directory tree for your ebuilds. Then you can share your tree with others. That's the gentoo way.