Just to let you know, we are expecting to carry out some maintenance on the new vADC community over the next few days, so this post may become inaccessible for a while. If you need urgent assistance, then either raise a support call, or else send me a direct email at "pwallace - at - brocade dot com"
I think this would be possible - the acme.sh script can issue certificates with multiple names:
acme.sh --issue -d example.com -d www.example.com -d cp.example.com -w /home/wwwroot/example.com
However, you would need to modify the other script to accept multiple arguments and pass to acme.sh.