Is there a right or wrong side that needs to be face up when applying cement board? An instruction book said to have the rough side up, however there are dots on what I would consider the smoother side that look to be where you would put the backer screws. Does it matter? I only have one piece down and I'd like to know before I mess the whole thing up. Thanks to anyone who can help.

Is this Duarock, Hardiboard or Hardi backer? You put screw where ever you need them, dictated by what you are attaching too, not by markings on the cement board. You expose the rough side if you are covering the cement board with thin set cement and tile. You expose the smooth side if you are covering with a adhesive and say a fiberglass tub or shower surround. What's your application?

hkstroud summed it up perfectly.