Look here: http://www.howtoforge.com/perfect-se...ispconfig-3-p6
If you didn't initially install an SSL certificate when you installed ISPConfig 3, you can do it by:
tar xfz ISPConfig-3-stable.tar.gz
php -q update.php
When it asks you if you want to generate an SSL, do it. AND make sure you put:
Common Name (eg, YOUR name) : www.asies-consulting.com
Or whatever your domain is...
THIS PROBABLY WON'T WORK UNLESS YOU CAN PROVIDE ALL OF YOUR csr, key, crt, etc, SO BACK STUFF UP! If you already generated a CSR forget everything I said above. If you generated a CSR, locate the ISPConfig cert files, and replace the CSR with the one you generated and the CRT with the one from Godaddy.
I hope this makes sense... If not, take a look at this howto, and it might help...