Schwarzbier is one style where I would aim to get just the color from the malts (obviously, you can't avoid possible flavor, but my goal is color first and foremost). I would add them after the last decoction in this scenario. In the case of something like a dopplebock, I would not shy away from having the dark malts roll through the decoctions.
Good on you for trying the decoction route! I had several great beers brewed with decoctions.