We stretch the cover over the pool then screw "U" hooks in the deck to hook through the grommets in the cover. When I say "U" hooks, I mean the kind you would use to hang coffee cups from by the handles in your kitchen. We tried using weights to hold the cover down the first year and it didn't work. The rain eventually pulled it down into the pool. Try to find aluminum, stainless or brass hooks. Those wont rust and leave stains on the deck.
We use the winch and wire method of securing the cover to the pool and along with that we also use gallon jugs filled with water and hang those on the grommets. We have used the bungee cords and try to get them long enough to allow the water jugs (MT bleach bottles) to touch the ground. I swear I am going to come up with something to stick in the ground and attach the bungee to that instead of messing with those darned jugs...
Our deck is about an inch away from the pool so we (I) have to crawl under the deck and try and pull the cover down over the railing while DH is on the outside messing with the cord. We even put water jugs on the cover under the decking. It is a real PIA to contort my body into the position it needs to be so that I can get under the deck, pull the cover, attach a water jug and NOT hit my head or back as I am duck walking my way around the underside of the deck.
I wish our deck went all the way around so that we could just screw it to the top of the deck and be done with it.
Ideally you want to leave room between the deck and the pool to avoid this issue but when it can not be avoided the cover is unlaced in that section where the deck is and the winch and wire are secured under the deck. The large flap of cover that can be tucked under the deck is laid flat and secured with water tubes