If you look at the EVGA licensed EKWB's you'll see the black metal logo plate has been laser cut and overlays the plexi underneath. This is really the only way to do it, see my suggestion above using vinyl. If you screw it up you only have to unpeel it and start again.
The more pieces you have to a water block the higher the chance of leaks. If the bulk of the block top was black with clear sections for the flow, it would have to have to be covered in screws to keep it all watertight. At that point it will start to look ****