Joining two composite decking boards side by side
The answer that you are looking for is... there is no answer. 

You will not keep the rain from migrating under the deck boards. That is the reason the framing for decks are done (or should be) in a rot resistant wood. If you wish to add another layer of protection, remove the deck in the area you wish to further protect. It should be easy since it is screwed down, and cover all the tops of the framing you wish to protect with a "peel and stick" membrane that also seals around any penetrations. This product is usually used for flashing around windows and doors when they are installed in their rough openings. It comes in rolls 6" wide or wider, but you can slice it into 3" widths to cap over 1 1/2" wide tops or use it full width on the 3" backer under the joint in question. The sticky material also seals around any screws you put through it so no water penetrates through where the screws are. Here is a link that shows how it is used on a deck. It is a few pages down on the pdf.