Surprised no one is commenting that their software has really poor usability. It may work well in providing secure certificates, but setup is a PITA and the documentation is abysmal.
Recently I had to renew that site again (I've been postponing and dreading it) and looked for a different client. The getssl bash script[1] had its own problems (all caused by me not taking the time to read the readme, but the default settings were a bit odd), but overall a 10× better experience than the official client. Much less magic, much more a unix-like tool ("it does only one thing, and one thing very well").
Fortunately, the certonly script grabs the cert and puts it in an easy location. Updating the config from there is easy enough.
1. Install the app. 2. Run the certonly script, following the prompts. 3. Point the server at the certificates.
The only hitch was stopping Nginx long enough to do the domain verification. A three line bash script fixed that.