When deploying vSphere Infrastructure Navigator (VIN), it is automatically associated with the vCenter Server from which it was deployed from and this behavior is by design. This means if you have two vCenter Servers, you will need to deploy two separate VIN instances, one for each vCenter Server as shown in the diagram below.
For scenarios where you have a separate management and compute cluster, each with their own vCenter Server, it can pose a problem if you want to run all your "infrastructure" virtual machines in the management cluster and not in the compute cluster. This very topic was recently brought up in an internal discussion and after explaining how VIN works, I safely assumed this behavior could not be modified. It turns out the discussion peaked the interest of one of the VIN developers and a suggestion was made on how one could potentially change this behavior. This un-tested (NotSupported) "workaround" would allow a user to deploy a single VIN instance under the management cluster and allow it to associate with another vCenter Server and its workloads. Below is a diagram on what this would look like.