From official support perspective running multiple instances of Portfolio Server 2007 on single server is not a supported scenario. Even the setup program for the tool has no way to achieve the same.
But from development and testing perspective sometimes it is more than handy to run multiple instance on same server (especially when you want the instance to have same set of configuration / customization).
Follow the small tricks below to achieve the same:
Copy the PPS 2007 ASP.NET application folder manually and publish that as a separate virtual directory or web site.
Copy the 'PPSAccountIndex ' and 'PPSAccountData' database (or use SQL backup / restore options)
In the newly created 'PPSAccountIndex' database update the database name of newly created 'PPSAccountdata' database
Modify the config files on the newly created virtual folder to point to new folder paths and new database.
Ensure only one copy of the Scheduler service is running on one physical machine, and additional PPS instances should be added in the principal (and only) scheduler config file.
Please check the licensing requirement with local licensing expert and this is not an supported scenario.