Please note, there are some domain and subdomain limits that are enforced by Let's Encrypt that we attempt to outline here:
https://documentation.cpanel.net/display/ALD/Manage+AutoSSL
If all goes well, we will be adding this plugin to the list of plugins provided in the WHM interface in cPanel & WHM version 60.
I want to mention, the most commonly requested feature in relation to this, SNI support for cpsrvd (which includes webmail, cPanel, WHM, etc) is being tracked in this feature request, and *may* make it in to cPanel & WHM version 60, but may be delayed to version 62:
https://features.cpanel.net/topic/ssl-certificate-per-domain-on-all-services