Since you have used the web interface, you could for example grab the latest Crypt::LE Windows binary and run it interactively (it can be also run in automated mode) with something like this to get the certificate for multiple domains:
le64.exe -email "admin@your.email" -key account.key -csr domain.csr -csr-key domain.key -crt domain.crt -domains "domain1,domain2,domain3" -generate-missing -live
Or like this to get a wildcard:
le64.exe -email "admin@your.email" -key account.key -csr domain.csr -csr-key domain.key -crt domain.crt -domains "domain,*.domain" -handle-as dns -generate-missing -live
Notice that in the latter case, with wildcards, you need to be able to control your DNS records. Also because the wildcard does not cover the “bare” domain (as in “mydomain.com”), in the example above you specify both with the -domains option. Full documentation can be found here or here (shortcut).