When it comes to certificates not generated by CWP, you're going to find you'll have a difficult time. Your website configuration can be overwritten quite a bit, and you will have to recreate what you've done. I'd recommend creating new templates for that domain only in /usr/local/cwpsrv/htdocs/resources/conf/web_servers/vhosts/nginx/ for that specific domain, so that your settings aren't overwritten.
As to why it's insecure, it's hard to tell unless you give us the actual domain name so we can look at it.