Can you modify the settings.php file using drush? I am trying to create multisites and the first one is up fine and running.  I am trying to use drush to install a 2nd site but I need the settings.php file to point to a different db.  Can I modify my drush command to do that or am I going to have to modify the settings.php by hand each time?

sudo drush -y site-install standard --db-url=mysql://$username:$pass@127.0.0.1:3306/$dbname --site-name="$sitename" --sites-subdir="$sitename"
What you really need here is different settings.php files for your production and development environments.

There are multiple ways of achieving this, some examples:


Setting various environments (development, production) based on the URL
Environment Specific settings.php Overrides


I usually include the following lines at the end of the settings.php file (in all instances):

// Override settings in this file.
if (file_exists('./' . conf_path() . '/local_settings.php')) {
  include_once './' . conf_path() . '/local_settings.php';
}


And then change the $databases array there, and any other specific environment settings.

You may also find useful the following links:


Defining variables in a site's settings.php $conf array
Set Environment module, that helps maintaining multiple environments with drush.