The upgrade tool is PubUpgrade.exe and it is installed with QVS9. The documentation for use can be found in section 24.1 of the QVS Ref Guide.
If your 8.5 is using SQL Server for the repository, I recommend migrating the repository to XML before installing 9. Then run the PubUpgrade and convert back to Sql Server if desired.
The upgrade process is described in the QlikView Server manual.
I highly recommend that you read this portion of the manual before proceeding with the upgrade.
To answer your question, the Publisher upgrade tool is located in the Publisher directory (can't recall the exact file patch but n one of the sub folders of X:\Program Files\QlikView\Publisher).
You will need to run the Publisher upgrade tool to convert the 8.5 QVPR database to version 9.
When this is done things should kick into gear.