Set the box on a flat surface with the open side facing front. Paint the inside back surface of the box to create the background for your diorama. Paint the sky, a mountain or two in the background and some low brush or desert terrain for the ground. Allow the paint to dry according to label instructions.
Cover part of your work surface with the wax paper. Roll out some of the modeling clay to a 1/2-inch thickness. Cut out a rectangle for the main body of your mission building; trim the clay to make curved or shaped edges. Cut a long, low piece of clay to serve as a fence across the front of the mission. Allow the clay pieces to dry completely according to package instructions. Paint the pieces if desired -- adobe brick or dazzling white were the standard mission colors.
Cut out a tall, narrow piece of clay for the bell tower. Cut out a rectangular hole at the top of the bell tower where the bell will hang. Poke a small piece of wire into the top side of the bell space. When this piece of clay has dried completely, carefully hang the bell in the opening by threading the wire through the top and twisting it to keep it in place.
Glue the dried mission building to the back center of the diorama box. Glue the fence piece widthwise across the box 2 to 3 inches in front of the mission building. Glue the bell tower assembly onto the back of the diorama to one side of the mission building.
Decorate your terrain by gluing on some sand to the foreground. Cut a few small trees out of plastic foam and paint them green. Use pieces of toothpick or skewer for the trunks. Glue the trees to the floor of the display.
Complete your mission diorama by making two crosses out of pieces of toothpicks or wooden skewers. Glue one cross on the center top of the mission building and another on top of the bell tower.