If you'd like to have enclosed storage there, it looks like it would work best against the back left side of the house (since right side appears to have a utility). It could extend from near the window to near the edge of the house and out just a few feet off the house so the majority of the area under the deck could be turned into an outdoor entertaining area.

I am trying to decide what kind of material to use to close it in...

How much space do you want for storage?

Ideally as much as possible... Planning to cement the floor..had hoped to eventually take out window and replace with a door to basement... Also trying to design stairs and where to place them.. The upper deck will be entirely screened... I originally thought I would have a center staircase not rethinking of having stairs come off the side

You seem to be building from the top down, instead of from the bottom up.

Should be looking at this as a room on the lower floor with a deck above.

The room surely needs to be watertight.

Who is building the deck? Are they involved with the lower level project?

PPF you have a point but what we need is storage space not another room in the house....

You want weatherproof storage, what you need is a space with walls, a roof and floor. The walls and floor are easy. It's the roof that needs the attention.

You have already made it difficult by building what you have. You would normally build the lower floor with a roof designed to have the deck surface placed on it. Everything is integrated, and because you want to connect with the house, the structure would be built just like another room in the house.

My advice is to talk with your contractor.