If you cover the deck, you'll still have splintering and warping, both which will either come through your 'cover' or be felt by your feet when you walk on it.
Also, unless your deck is, say, at least 3' off the ground where the 'skirt' is NOT largly obstructed with plants and/or lattice (perhaps), the cover will prevent the ground underneath from staying dry. In other words, some folks whose decks are about 3' off the ground plant bushes and such all around their decks. And, they may even run some lattice around the 'edges' of it too so you don't see underneath. Yes, it looks nice but these 2 types of 'cosmetic' additions prevent airflow under the deck. Airflow is what transports the moisture to the 'outside' that rises up from the ground. If you cover your deck, you'll have all kinds of new problems. (Most likely, whatever you cover your deck with, will rot over time. Plus, you'll have mold/mildew and odor problems too. PT wood will rapidy deteriorate under these conditions.)
My suggestion is to replace the bad boards. Or, consider a different type of deck-material. If your deck is relatively small, then you should look into a maintenance-free material, like Trek-Deck. I've attached a few posts that talk about fixing the deck and alternative materials. If you need more, post up or e-mail me directly. My best to ya and hope this helps.