How to apply patches?
If you're on UNIX based system (e.g. MacOSX, various Linux distros), the patch utility is a great tool here. I typically use the command: 

patch -p1 &lt; patch-file.patch


With the -p1 option being important for installs already under a git repo.

It sounds like your use case is a bit different though. drupal.org has a good documentation page for applying patches in various environments.