Add Support for multiple databases

Where would I put that code?

I think it would be better if that code were in this module (I.E. Submit that code as a patch to be committed) so I could use this module's web front end to analyze my secondary database.

I still think it is a valid feature request to support more than one database connection.
All the database connections are saved to $db_url variable in the settings.php file. We could use that variable to add a new select box form element to the web front end. That would give the user a way to select between the default database or use a secondary database connection

  global $db_url;
  $form["database-connections"] = array(
    '#type' => 'select',
    '#options' => $db_url,
    '#default_value' => 'default',
  );
 

Then switch to the database in the form submit call

  db_set_active($form_state['values']['database-connections']);
  .
  .
  .
  db_set_active('default');

I worked out a patch and tested it with my multi database setup. This allows schema module to work with more than just the default database connection.
You have to set up your secondary database connection in your settings.php file for this to work.