There are several factors to consider. In mojoPortal there is a Web.config setting for SSLIsAvailable, since that is global to the installation then of course it would impact all sites in the installation and if set to true on a site without a matching ssl certificate it will cause problems.
But the bigger issue is that you cannot easily bind more than one ssl certificate to a single site in IIS on a single ip address.
So the easiest solution would be to split off the site(s) that you have ssl certificates for into separate installations.
If you have an ssl certificate for each and every domain there may be ways to bind them each with different host names on a single IIS site but I think that only works if each of the certificates is a wildcard certificate.
If you have certificates for every domain but they are not wildcard certificates then one other possible way is to create an IIS site for each domain but point them all to the same installation folder.
But all of that is tricky stuff, the easiest way is going to be to split the sites with certificates into their own copy of the installation. You can still use the same database for each site or you could backup the db and restore different copies for each site.
Hope that helps,