I think I do understand what certonly does, but this is a support forum, so if my understanding is incorrect I hope someone would help me improve that.
My understanding, and from https://certbot.eff.org/docs/using.html#getting-certificates-and-choosing-plugins, is that certonly loads the certificate to the server, but does not update the apache configuration files (see Autorenew vhost ambiguity if interested). At least I think that is what is meant by “install”.
I was forced to do use certonly when I first started working with letsencrypt because the apache plugin wasn’t working correctly. I have my own work instructions now on how to edit the apache vhost configuration file and restart the web server after running certbot. Probably I don’t need the --apache switch, so maybe that’s what is causing some confusion on the part of @rg305 of what I am doing and why. And possibly I don’t need to use certonly any more. But my process seems to work and I don’t have a lot of time to play with this because I need to move forward with the process of creating this vhost and the application which will live on it.
In any case I have 8 vhosts running on this server by doing what I have been doing, all appearing to work fine with ssl.
It seems like the current localhost.crt file I have can’t be used because it expired in March. /etc/httpd/conf.d/ssl.conf references localhost.crt and localhost.key. Not sure where I configured the server itself to “be” loutilities.com but I’ll figure that out. It’s possible that was only in the localhost.crt/key files.