Apart from what SirDice says (which is very correct, 8.4 is ancient and running it is insane ...)
The base FreeBSD operating system does not use a SSL certificate (they are typically not called TLS certificates). Certain servers can use the certificates. The most common server to need a certificate is probably Apache. The certificates can be stored many places; since I use LetsEncrypt for my certificates, mine are stored in /usr/local/etc/letencrypt/... in several subdirectories. The important part is that the Apache configuration in /usr/local/etc/apache24/extra/httpd-ssl.conf points at those certificates. There are other servers that may need certificates (e-mail ...), which all have configuration files that point at the certificates.
All this has very little to do with proxies, and with environment variables. As far as I understand, configuring a proxy helps the web browser, not the server.