I always take the ply lining out of our vans. Once they're Protektacoted, I don't like covering it up again, and certainly not driving screws through the Protektacote to attach the lining - water will track along the fixings and rot around the threads.
I put loose ply sheets on the van bed to save the Protektacote from gouges and regularly lift them to give the van bed chance to dry out.