Drush unable to find settings.php
First off, you should not call drush.php directly; use the drush script instead.

Regarding site selection, Drupal looks up the site to use based on the domain name in the http request, which is passed in via the HTTP headers.  When you are using Drush, there is no web browser involved, so Drush needs to generate equivalent HTTP headers and select the appropriate site based on information that is provided either explicitly (via commandline options) or implicitly (via the current working directory).

If your cwd is inside your Drupal root, then Drush will, by default, look for the settings.php file inside the 'default' folder.  You can change this default by setting your cwd to the folder that contains the settings.php file that you want, or by passing in --uri=mydrupalsite.com as a commandline option (or -l mydrupalsite.com).  You might also want to read up on Drupal site aliases, which are an even more convenient way to tell Drush which Drupal site you'd like to use with your command.