Should I render the workarea/sequence in Premiere Pro CS4, or can I render the video in Encore? So does Encore know it should use the Neat Video filter that's been used in Premiere?
I recommend to render everything in Premiere, not in Encore, to make sure the actual burning is done at the burner speed, not at the render speed, which may be lower than burner speed.
Unfortunately I don't have Encore on my computer to directly test that. If Premiere's own filters are applied in Encore then third-party filters (like NV) will most likely be appled too. Please test that on your computer by rendering a small test clip to a folder.