Draw two medium-sized square windows on each gift box with a pencil. Paint each box deep brown without coloring the windows. Set aside all three boxes for 25 minutes to allow them to dry.
Use sharp scissors to cut out 4-by-6, 3-by-5 and 2-by-4 rectangles from the cardstock. These will be used as the overhanging roofs which appear on most Japanese pagodas. Paint all three sheets a lighter shade of brown to offset the deep brown hue of the boxes. Lay aside to dry.
Set the 4-by-4 inch box as the base of the pagoda. Apply a strip of glue to the bottom of the 4-by-6 inch piece of cardstock and paste it on top of the 4-by-4 box. Glue the 3-by-3 inch box on top of the 4-by-6 inch cardstock. Glue the 3-by-5 inch cardstock on top of the 3-by-3 inch box. Then, glue the 2-by-1 inch box on top of the 3-by-5 inch piece of cardstock. Paste the final cardstock, the 2-by-4 piece, on top of the 2-by-1 inch box.
Allow your pagoda structure to dry for at least 30 minutes.