For each site that you want to use separate database, create own sites/ directory with settings.php. For example, if you want to have one database for example.com, another one for sub1.example.com and third one for sub2.example.com, all using same code base, setup your files like this:
sites/example.com/settings.php
sites/sub1.example.com/settings.php
sites/sub2.example.com/settings.php
each settings.php using different database credentials. Read more here - https://drupal.org/documentation/install/multi-site
Also, if you want to automate this and if there is supposed to be bigger number of sites to be managed, consider deploying aegir - http://www.aegirproject.org.
I hope I understood your question correctly.