Since last I have attached some magnets to the lower side of the lower deck, to keep the upper deck in place. Normal CA wouldn't really hold them in place, so I decided to use silicone. I also decided to put silicone all around the magnets to protect them from water. this can be seen in the pictures below. Then I'll use washers on the lower side of the upper deck.
I also found an item that will stop water from coming in at the places I intend to use the guns for fixing the deck in place. Finally I made a boat stand. The boat stand was done quickly and nothing to show off, but it will do for now.
The next step will be to get the boat balanced and get the lower deck fixed.
Have a look at the pictures: