I created a schematic using world edit, transferred the file into the proper folder in chance cubes and loaded it via the Schematic command. It created a prismarine box, but the schematic was for a dark prismarine box. I loaded the schematic via world edit and world edit created a dark prismarine box.

Command:
"Schematic": [ {"fileName":"darkprispool.schematic","RelativeToPlayer":true } ]

Schematic: Attached
darkprispool.zip

I will look and seem if the schematic file format has changed since I first implemented it. In the mean time i would recommend you convert in to my custom schematic system as it is much more stable and support by chance cube than the regular schematic system is. I have a video explain the process a bit here https://youtu.be/c91CoNaLz9E?t=1m35s