Set up the job to your liking, including selecting Silver Efex from the Open With popup menu (see the top illustration).
Right-click on the RAW file and select Edit With.
By doing so, the original image will stay protected.
In Capture One Pro, start with a RAW file.
A new file is created from the original RAW, and it is sent to Silver Efex for work. Going this route allows you to set up an Edit Recipe, where you can choose between Tiff or Jpeg, color space, resolution, and scale. Start with the Edit With command in Capture One Pro. Capture One Pro can connect with that app using the Edit With command: Control-Click > Edit With > Silver Efex Pro 2. What you might not realize is that, even though you've been using Sliver Efex Pro 2 as a plugin, there's an app in your Applications folder: Applications > Nik Collection > Silver Efex Pro 2.app. This also works for other apps/plugins too. I've been using Silver Efex Pro with Capture One, and the two get along just fine. Just because you left Aperture or Lightroom behind, that doesn't mean that you have to abandon your favorite plugins too.