The FMS instructions on creating a certificate are quite a pain and I couldn't get it to work. See the certificate command line instructions on page 171 of http://www.filemaker.com/support/product/docs/12/fms/fms12_help.pdf
This is a development server of mine I have running various things from DNSs to web pages. When I ran the FMS 13 install, it set up its on web services and shut off the Web pages I had turned on. No big deal since this is a devleopment machine and the web pages I had were just test one. Then I started using my development machine to do some registrations of a conference for a non-profit I volunteer with. Here is an example of a bad idea of using your development machine to help a non-profit out and thereby making a production environment out of your test bed. I know... know.... bad practice.
I went to GoDaddy to get a Certificate (I have a wildcard one, so just using one of my available wild cards). It installed no problem other than GoDaddy doesn't know anything about a Mac OS X Server beyond version 10.6. But I found a good video about installing certificates on a Mac 10.8 at http://www.macstadium.com/blog/hosted-osx-mountain-lion-server-part-5-ssl-certificates/
I got the certificate installed and all looked good on my Mac. Except, remember, FileMaker made its own web services thing and it did not recognize the certificate I installed and that all other services on the computer were using. Hmmmm.... frustrating. After trying to install the certificate the FileMaker way, I gave up, just went to the Server.app, turned on web services. Presto, the valid certificate for the whole server suddenly started being used by FileMaker service and I can now direct people to my Web Direct web page without them getting that silly certificate warning.
By the way, GoDaddy may be OK for a wildcard, but for SSL certirficates, they are a bit expensive. Their standard one is like $69.99 and they have a much better one for $149. Save some money and go to www.namecheap.com and get a basic SSL certificate for $8.95. That's all you need so people don't get that SSL warning when going to your WebDirect pages.