Hi Dave,
A single installation of mojoPortal can do either multiple sites based on host names or multiple sites based on folder names, it cannot do both. You would need two installations one for folder sites and one for host name based sites.
For folder based sites the first site must be a root level site it cannot run as a subfloder beneath an IIS web site so you would first get it working at http://mojoportal/ ot http://whateverhostnameyouchoose/ using previosu instructions I've given you
and even for host name based sites it doesn't make sense to use subfolders so host name based mutliple sites needs to be first installed as a root level IIS web site., again with instructions I've given you you would first get it working at http://mojoportal/ or really at http://whateveryouwant/
Then if you are going with host name based sites you need to add additional host names to your hosts file for each one, ie
site1 127.0.0.1
site2 127.0.0.1
whateveryouwant 127.0.0.1
and also add those host names in the new IIS web site as host names otherwise IIS will resolve any host names not specifically assigned to a site will resolve to the default web site which has no host names
so after you create the site depending on which approach is configure you will see in site settings either a tab for assigning host names to a site in mojoPortal or assigning folder names, you enter the host name or folder name there.
if using host names then you access the sites using http://site1/ or http://site2/ ie whatever host names you used.
if using folder sites you access the sites with
http://mojoportal/foldername/Default.aspx
or
http://whateverhostnameyouused/foldername/Default.aspx
Hope that helps,
Joe