The help files with the product are, unfortunately, piss poor, as you no doubt have found out. I have some good news and some bad news.
1. The certificate service is fairly easy to create certs for SSL. The help file is fairly decent on this.
2. The bad news is that you will have to ship out a file for the cert to everyone who accesses your site. This is due to the fact that the cert does not map to a third party like Verisign, whom IE and NS trust.
My advice:
Get a cert from Verisign(or another trusted party), unless this is for your employees only. If this is an e-commerce initiative, the fact that your cert is not trusted will cost more in lost revenues than the few hundred dollars you will spend for a cert.
If you want togo ahead with the certificate service on IIS 4, I have done this and can help. You will have to trust me that it is a pain in the butt to implement, and really not worth it.
By the way, setting up the certificate service on the IIS box is simple,but a true CS certificate (which can sign certs for other clients) is considerably more expensive than a simple SSL cert.
I hate to be the bearer of bad tidings, but these are the breaks in the e-world.
Gregory A. Beamer
MCP: +I, SE, SD, DBA