I recently purchased a new home.The deck looked fine,but when summer came everyone was getting splinters in there feet.Is there anyway to fix this without replacing the deck?

I am in the process of adding a screen porch, with a deck above. I would like to make the screen porch waterproof and use bead board for the ceiling. I have used the corrugated plastic for drainage between the deck and the screen porch and placed it on an incline. After a fairly lengthy rain two nights ago there were some leaks (nothing major, but will ruin bead board) at the seams where corrugated overlaps and some water standing in the middle next to seams. My question is simply is there another method that I should look at? I am still in the construction phase and could change directions if necessary. Or am I on the right track and just need to silicone the devil out of the seams?