BI Publisher is mainly a reporting tool from Oracle. How we use it in Agile 9.3.1 – it has SQL Query that works on the Agile DB to pull out reports and email them. It needs Agile DB username/password and connection string to connect to Agile DB.
It is useful for certain reports that cannot be pulled out from Agile Advanced Search or for external users without access to Agile.
I found a link to set up layouts in BI Publisher: http://docs.oracle.com/cd/E10091_01/doc/bip.1013/b40017/T421739T423025.htm#4511636
Hope this helps.