If you have added modules or themes to your Drupal site or manually installed the original software, you'll have to manage your software updates manually. To update Drupal, follow these steps:
Back up your database.
Copy your entire Drupal site to another location.
Don't make a copy of your Drupal site and store it inside your Drupal site. Make sure your backup copy is outside of your entire Drupal directory — preferably not even on the same web server. You can always upload the copy back to the web server later if you need to.
Choose Configuration→Development→Maintenance mode and select the Put Site into Maintenance Mode check box.
Click Save Configuration.
Click Modules and deselect any contributed modules. Leave the Core module settings as they are.
Click Appearance and choose one of the themes that was installed with Drupal originally, such as Garland.
Get the new version of Drupal from drupal.org.
Use a file manager or FTP program to copy the new files to your Drupal directory, with the exception of the sites folder.
Do not overwrite or copy over this folder with the new files.
If you browse to your site right now, you’ll see the original installation when you install Drupal. Do not run this program. You’re updating, not installing — and running an installation can destroy information stored in your database.
Browse to the update.php on your website and click through the installation screens.
Choose Appearance, and then choose your desired theme.
Choose Modules and enable any contributed modules you want to use. Leave the Core module settings as they are.
Browse to the update.php on your website and click through the installation screens again.
It's important to run update.php every time you install a contributed module. Because this is the first time this new Drupal codebase is using the modules, it treats them like a new installation.
Choose Configuration→Development→Maintenance mode and deselect the Put Site into Maintenance Mode check box.
Click Save Configuration.
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Source:http://www.dummies.com/how-to/content/update-manually-installed-enhanced-drupal-software.html
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