Installing Letsencrypt on a cPanel server with apache and nginx running together

Server
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  1. I tried the installation by following the steps given at https://forums.cpanel.net/threads/how-to-installing-ssl-from-lets-encrypt.513621 . But when I execute the command (after replacing by username and domian name)

./letsencrypt-auto --text --agree-tos --email email@domain.com certonly --renew-by-default --webroot --webroot-path /home/cPanelUser/public_html/ -d domain.com -d www.domain.com

I am receiving the error

=====================
x The program nginx (process ID 1687) is already listening on TCP port x
x 80. This will prevent us from binding to that port. Please stop the x
x nginx program temporarily and then try again.

At least one of the (possibly) required ports is already taken.

I am running both apache and nginx together. Apache on port 8081 and nginx on port 80.

  1. Another query is that I am having Drupal multisites with nearly 12 sites running under one single drupal installation. So is it possible to install your cert for these sites?