.gitconfig is a global configuration file that resides in your HOMEDIR.
.git is your special directory in any git repo that makes it a 'repo'.
Inside .git is a file called config that applies all the configurations mentioned in it to that particular repository only.
You can add configurations to either .gitconfig/.git/config using the git config command.
Eg:
git config user.name "Jane Doe" adds a user.name entry in your current repository's .git/config file
git config --global user.email "jane.doe@example.com" adds a user.email entry in your users .gitconfig file, and it will be applicable to all repos under that users.
(Note use of --global)
Using mysysgit has a lot of benefits. Cygwin is also a good option!
Cheers!
