What I did in IIS was created a new website, then I change the application pool to .NET v4.0, the port to 8081, and change the physical path to the folder where the Bonobo Servers would be extracted to.
Once I extracted the servers to the folder. Once they were extracted I followed the instructions on the site. So Bonobo.Git.Server and Bonobo.Git.Server.Interface where both converted to applications.