Welcome here!
renchap has written a tutorial to automate certificate renewal for Nginx (even for all your other applications, it will work) : Howto: easy cert generation and renewal with nginx
As you may have noticed, all the files in /etc/letsencrypt/live/domain.tld/ are just symlinks to the files in /etc/letsencrypt/archive/domain.tld/
Whenever the script runs (and generates the certificates), the certs in /etc/letsencrypt/live/domain.tld/ will be replaced, but their name will not change; it makes it perfect for automation, because nothing will need to be reconfigured.
Have fun with letsencrypt!