This is slightly different from the standard instructions although most of the standard instructions will apply. It is different because
Please refer to Creating WordPress Websites for adding new WordPress websites
To do the manual upgrade usually requires you simply overwrite the new WP files. Check the latest version upgrade instructions to be sure. Once that is done you can log on to each site and click upgrade to upgrade the database. Below is a SQL script to help you check the version of all your wordpress sites
Use this SQL to check in one go. Include more lines as required of course!
SELECT 'wp01_options' TABLE_NAME, option_value FROM wp01_options WHERE option_name = 'db_version' UNION ALL SELECT 'wp02_options' TABLE_NAME, option_value FROM wp02_options WHERE option_name = 'db_version' UNION ALL SELECT 'wp03_options' TABLE_NAME, option_value FROM wp03_options WHERE option_name = 'db_version' UNION ALL SELECT 'wp04_options' TABLE_NAME, option_value FROM wp04_options WHERE option_name = 'db_version' UNION ALL SELECT 'wp05_options' TABLE_NAME, option_value FROM wp05_options WHERE option_name = 'db_version' UNION ALL SELECT 'wp06_options' TABLE_NAME, option_value FROM wp06_options WHERE option_name = 'db_version' UNION ALL SELECT 'wp07_options' TABLE_NAME, option_value FROM wp07_options WHERE option_name = 'db_version' UNION ALL SELECT 'wp10_options' TABLE_NAME, option_value FROM wp10_options WHERE option_name = 'db_version' UNION ALL SELECT 'wp11_options' TABLE_NAME, option_value FROM wp11_options WHERE option_name = 'db_version'; ...
Below are steps to completing the upgrade
cd /www/path/to/wordpress/..
rm latest*.zip
wget "http://wordpress.org/latest.zip"
cd wordpress/wp-includes
find .|grep -v "\.svn"|xargs rm
cd ../wp-admin
find .|grep -v "\.svn"|xargs rm
cd ../..
unzip latest.zip
cd wordpress
svn status
svn status|grep "^\!"|awk '{print $2}'|xargs svn del
svn status|grep "^?"|awk '{print $2}'|xargs svn add
svn commit -m "Upgraded WordPress"
cd ..
chown -R www-data:www-data wordpress