Q: How do I install self-signed SSL certificates on two IIS 6 websites on the same server where both sites use port 443 and are configured with host headers?

A: Multiple SSL sites on a single IIS server using host headers.  <- the answer. 

Basically, use SelfSSL or SSLDiag to create a cert with CN=*.example.com, then just point the second site to that cert in the Directory Security tab.  Also, configure secure server bindings using adsutil (found in c:\inetpub\adminscripts).