Welcome to the Let's Encrypt Community! 
Just use CertSage and save yourself a lot of time and effort.
Note: I am in the process of writing a step-by-step, illustrated tutorial for using CertSage for multiple domain names hosted within a single cPanel account. I expect to publish it early this coming week. You can still use CertSage right now to very quickly acquire and install your new certificates to keep your sites up and running then make a couple of tweaks next week to have CertSage setup to automatically renew all your certs from now on.