I've used this workflow w/ no trouble in the past:
1. Already have a running website I don't want to mess up.
2. Create a subdirectory in there and upload Drupal.
3. Create a new database in MySQL.
4. Set the site up using the default site's settings.php.
5. Once I'm done, zipping up the old site/removing it from the server.
6. Moving the code from the subdirectory to the document root.
7. Browsing around to make sure everything is fine.You really just need to look out for hard coding paths in your nodes. Everything else should be handled relative to the Drupal index.php so you shouldn't have to change a thing...
Joined: 08/07/2007