I am running owncloud in a docker on my unraid server and recently setup letsecrypt. I have the certificate.pem files and I would like to exchange them with my owncloud self signed certificate. How would I do that? Seems like I can't find a how to on Google. Thanks.
ownCloud is just a web application written in PHP and doesn't handle any SSL/TLS (besides the ones for outgoing connections). This is your webservers job. Searching on the net outside of the scope of ownCloud should give you tons of information how to configure this on your environment. Quite good tutorials are e.g. the ones of digital ocean .
As you're running docker this is also another specific thing unrelated to ownCloud. Maybe the documentation of your docker image (if this was a prebuild one) has some additional information how to configure SSL/TLS within it.