I recently had to update one of the certificates running on a few of our systems as the one I replaced was set to expire. Most of the updates went very smoothly and quickly, but there was one instance that I ran into that required a bit of extra work. One of our web servers runs on a Server 2008 system running Server Core instead of the full install. What this means is that there is no GUI to do your work and all of your maintenance takes place either through command line or remote tools.
For some reason, I was unable to make my certificate changes using IIS7 running on another system (which may be another issue entirely). Because of this, I had to learn how to make my certificate changes via the command line on the server itself. I used the following link as a guide on how to complete this process. http://www.awesomeideas.net/post/2008/05/18/How-to-configure-SSL-on-IIS7-under-Windows-2008-Server-Core.aspx