Basically you can add separate instances of Q2A in sub-folders, then set the QA_MYSQL_USERS_PREFIX option on each.
Set up the main site first. In qa-config.php you'd have something like:
define('QA_MYSQL_TABLE_PREFIX', 'qa_');
Then copy all the files to a sub-folder or sub-domain (e.g. "meta") and in qa-config.php you would set:
define('QA_MYSQL_TABLE_PREFIX', 'qa_meta_');
define('QA_MYSQL_USERS_PREFIX', 'qa_');
Then go ahead and set up that instance of Q2A. Repeat for each sub community.
