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
sites/sites.php. Note that this is not necessary for "www."-style subdomains.
Update Drupal core, contrib projects and update database
Run command for specific site
To e.g. run updatedb for jabber.at:
drush -l jabber.at updatedb