If I want to replace the wood boards on my deck, will there be a problem installing new ones because of the existing screw holes? We would like to put composite boards in place of the old boards, but we ONLY want to do the top layer…not all of the wood framings.
This is a great project to take on whenever the existing deck boards have become cracked, rotted, or otherwise deteriorated. It will essentially allow you to have what looks to be a completely new deck, but while only having done part of the work. In this case, you will remove all of those old wood deck boards and replace that decking with composites. (Here is more information on composite decking.) You asked if you had to be concerned about lining up the previous screw holes. The answer is no, you absolutely do not.
The composites should be directly attached to the original floor joist, and keep in mind there are a number of ways to do just that. For example, composites offer a "hidden" attachment system where the deck screw fasteners are really hidden; they may be inserted into the sides of the boards or attached with special clips. It's well worth looking into this because the result is a much more attractive surface. If you are going to attach through the composites, special screws have been designed for this. They will drill and screw at the same time. This will avoid that "mushroom" effect - where the decking surface backs up around the screw as it passes through. If you pay attention to the attachment points, you will find that the entire project looks a lot neater.
While you're at it, you may want to think about replacing the wood railing and covering the exterior box beam. That's the wood that surrounds the outside of a floor joist structure. You don't actually have to replace it, but you can cover it with additional composite material. Composites are available in a standard 5/4 in. x 6 in. size for decking. But, they are also available in a 1 in. x 12 in. option, which is the perfect size to cover those sides of the deck. Either way, you're going to have a good looking deck that you can use for many more years.
As a first step, I should caution that I would inspect the deck carefully to make sure the floor joist is structurally sound and the deck is firmly attached to the house. You wouldn't want to go through all that work only to find that the structure is bad later. Here are more tips we recommend for repairing your deck! Good luck with that project, and send us pictures when you're done!