The source code for Drupal is stored in
/var/src/drupal. Every domain hosted has to have a symlink to it in
/var/www/<domain> (since Apache assumes the DocumentRoot is there).
All configuration (including uploaded files and possibly modules/themes that are only installed for one site) is located in
sites/<domain>/. Modules available to all sites are available in
sites/all/. The latter is also the default location where drush installes modules and themes.
Update Drupal core, contrib projects and update database
Run updatedb for specific site
drush -l updatedb