As long as the CGI scripts are able to execute properly, you can place the cgi & variables files in a diredtory other than cgi-bin. Or you can put the files in a sub-directory, such as cgi-bin/board.
Just be sure that the different installations in the different locations have their paths & URLs set so that they are pointing to the proper locations. Use whatever naming conventions you need to to keep them separate. As long as 2 licensed boards are running on 2 separate domains, with each using their own software (not shared), you should be fine.
