Installing SSL Cert from a directory outside of the domain's home directory

I already have the SSL certificate uploaded on my server and i want to add it to Virtualmin. The problem is that the directory of the certificate, is not in the home directory of the domain but in /etc/letsencrypt/.... How can i add it from the current directory, without copying the certificate in the home directory?

Further explanations just for background.

I was trying to add an SSL cert for my websites and i stumble upon the Letsencrypt free certificates. Researching for that, i saw that my hosting provider in collaboration with Letsencrypt, simplified the procedure of the issuing and updating the cert. (https://help.dreamhost.com/hc/en-us/articles/222168828-Setting-up-Let-s-...) i followed the instructions and created the cert which installed it in /etc/Letsencrypt directory. when i tried to add it on Virtualmin i saw that to be able to accept it, it must be in home directory of the domain. but if i copy the cert, i will break the auto update. (error i received "Failed to install certificate : Certificate file /etc/letsencrypt/live/domain.com/cert.pem must be under the virtual server's home directory")

In the meantime i saw that virtualmin also has auto creation and auto update of the Letsencrypt certs, but i can't use it now because it reports "...request failed. The native Let's Encrypt client was used previously on this system, and must be used for all future certificate request"

I dont know how to undo the procedure i used to issue one in the first place so i decided that the easiest solution is to create something like symlinks, but i cant find how.

Thank you