You can put mojoPortal in the root at www and other apps can run in virtual directories below root. That is the best solution if mojoPortal is going to be the main part of your site.
mojoPortal could also run in a virtual directory below root instead of directly in the root but in that case you cannot use it for your home page.
If the other apps are .NET apps, you may encounter conflicts between the Web.config settings of the root mojoPortal site and other apps, but these can be mitigated.
Hope it helps,