Since they've not put the manpage(s) on web, I'll take some time to look at the source files.
First, the command has "--help" option that will display all the switches available to you. And then there's "--domains" and "--server" option that could be useful for you. "--authkey" specifies the location of authorized key file. These settings are for commands "run" "auth" and "install".
The comments in source file also mentioned these settings are also configurable in the configuration file at "/etc/letsencrypt" (the name may vary sliently by the package manager... sometime they decide to add/remove hyphens in name... so if the file not exist please also seek for file with similar name)