Greg,
As far as I know PPS2006 can't create additional instances in the way
Project Server 2003 does with the EditSite Tool.
You would have to create a second virtual directoy for your second PPS2006
instance and also create additional databases on your SQL Server. Although
I'm not quite sure, I do think that you can use the same web site in IIS for
your 2nd instance.
Hope this helps...
Marc S.
MCP for EPM
www.diventis.ch
www.msepm.blogspot.com