The shiny side is the coating. You want to protect the coating by keeping it inside.
Shiny side in, dull side out.
FWIW Cordura, IME, isn't waterproof. My pack, with a 500D Cordura bottom, sat all night in a puddle of water from another hiker's leaking hydration reservoir. My pack was soaked through and my pack liner saved all my gear from the flood.