Wordpress Multisite, VirtualMin, and Let's Encrypt

So here is my current setup:

CentOS Server running various blogs that I am constantly updating. Everyone of them are using StartSSL certs, some are sub-domains and some are domains. I have decided to give multisite a go because I am getting more and more into making blogs and websites based off WordPress.

I am okay with using StartSSL because its not that much work to get the free cert for my domains and I don't create new ones that often. But I do want my sub-domains and domains to all use SSL. So my question is, what is the easiest (preferably automated) way of getting the domains on SSL?