The URL you (and your end user) typically use when accessing the portal via your browser should be used in the Integrated Authentication and the Base URL to Process Manager. For example, if I login to my portal with the following URL:
http://ServiceDesk/ProcessManager
I would want my Integrated Authentication URL to match (it would be something like):
http://ServiceDesk/ProcessManager/WindowsAuthentication.aspx
And my Base URL to Process Manager should be:
http://ServiceDesk/ProcessManager
Additionally, it is important for your default server setup to contain the same URL. From LocalMachineInfoEditor, edit the default server. In my example the Deployment Root URL would be:
http://ServiceDesk
Hopefully this makes sense!