We have a single installation of mojoPortal running 11 sites. In IIS, our mojoPortal installation is running as the default web site, so of course there is only a single app pool for it. Our multiple sites are defined by subdomain, so it's mojoPortal that decides which site to serve based on the host name mapping settings. I'm actually not sure why (and how) you would define multiple sites/app pools in IIS for a single mojoPortal installation with a single web.config file.
I hope that's useful to you.
Jamie