Drush Bootstrap Error on Multi-Site Install
There are several ways to specify which Drupal site Drush will target.  The most basic option is fairly verbose; run:

$ drush --root=/path/to/drupal --uri=http://mysite.com status


You can do the same thing with a slightly different syntax:

$ drush /path/to/drupal#mysite.com status


You can also specify the Drupal site implicitly, by setting the cwd to the folder that contains the settings.php file for your site:

cd /path/to/drupal/sites/default # or /path/to/drupal/sites/mysite.com, as appropriate

$ drush status


In all of the cases above, if settings.php is in a folder called "default", then you do not need to specify the --uri component; you may, for example, cd /path/to/drupal followed by drush status, and the correct Drupal site will be found.  If settings.php is not in a folder named 'default', then you will need to either specify --uri, or cd to the folder that contains the settings.php file.

You might also want to investigate Drush site aliases, which are another way to conveniently specify which site you'd like Drush to target.