What's the best practise to deploy new code on a live (e-commerce) site?

For now I have stopped apache for +/- 10 seconds when renaming directory public_html_new to public_html and old to public_html_old. This creates a short down-time, before I start Apache again.

The same question goes if using Git to pull the new repo to the live directory. Can I pull the repo while the site is active? And how about if I need to copy a DB as well?

During the tar (backup purpose) compression of the live site I noticed that changes occurred in the media directory. That indicated to me that files keep on changing periodically. And if these changes can interfere if Apache is not stopped during deployment.