Anyway, they wanted to install their own CA cert, from internal PKI, to remove SSL Certificate errors.
Alls you need to do is:
1. Save your root CA into PEM format and rename it as custom_CA.inc
cp cert.cer custom_CA.inc
2. Copy the custom_CA.inc to the Nessus lib plugins folder
sudo cp custom_CA.inc /opt/nessus/lib/nessus/plugins/
Now all those pesky SSL Certificate errors for internal network SSL based connections, wont appear in your results.
NOTE:- Dont do this for external SSL based services, you really should be using a SSL Cert signed by a recognised Certificate Authority (CA).
HTH