Create the subfolders on your server, and install a copy of Q2A in each one. (You could start messing about with symbolic links to have only one set of files but that's probably more complicated than necessary.)
Set up the qa-config.php file for each installation to be identical, except give each one a different value for QA_MYSQL_TABLE_PREFIX. Also move the following line in each qa-config.php outside of the comment:
This means the Q2A sites will share user tables, but otherwise keep their data separate.