It depends a bit on what you already have on your live site.

I think you should make a distinction between working on the source code 
using git repositories, and doing actual deployment of your site.

I think I would do something like this. First you want to set up a 
reproducable/scriptable routine for deploying your site the way it is today:

1) Copy your live server's files to a local directory called "site" or 
something
2) Initialize a git repo in this directory (cd site; git init)
3) Important: Take a backup of your live server's contents that you can 
restore if you want to go back to the old way.
4) Clear out the live server (or move the old contents away or something)
5) Publish the site git repo to your server, if possible use a tool for this 
like Capistrano <http://help.github.com/capistrano/>.

If you don't want to, or can't use Capistrano, you can use git 
archive<http://stackoverflow.com/questions/160608/how-to-do-a-git-export-like-svn-export>and
 upload the archive to the server and unpack it manually.

Once you've done this, you can start working on your local site repo and 
merge in the other changes you've been working on locally. And then repeat 
the deployment routine. Post back here when you get to this step and need 
more help.

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