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.
Domain aliases: If you want to make the same site available under two domains (e.g. like currently jabber.at, jabber.zone etc. are all the very same Drupal configuration), use
Update Drupal core, contrib projects and update database
Run updatedb for specific site
drush -l updatedb