Hi, I wouldn't remove the popcorn unless you HAVE to, because it can probably be messy. If it will cause unevenness, as Jay said, then yes. If not, don't bother. If the boards are tounge and groove or shiplap then stain before you put them up (if you are staining) and stain the edges or tounges because they might become visible later when they shrink. John 200's ideas are good too. Leave at least 1/2" gap all the way around the edge for possible expansion. Maybe cover it with a moulding or thin edge ripping tacked on. If you don't already have vapor barrier on the ceiling then you could put black plastic sheet up first.