repository in different directories

Hi, I'm using git to build a website using the Codeigniter php framework. I work on my local machine and then push to a remote server. The whole website would be divided in different directories. I have the webroot in /home/carlo/public_html/ directory. Here I have an index.php, the css files and images. Then, outside this directory, I have the application folder with all the real php stuff. Suppose it is in /home/carlo/ci/application.

I have the same configuration on the server. So, the workflow would be that I work on my local machine, I change something in the application folder, then something in some css file and then I have to sync everything with the server. I can have two repositories, one for the folder in the webroot and another one for the application folder, but then I'd have to push twice. Is there a better or a good way to do all this?

Thanks, Carlo