Paint your clay pots and trays with multi surface paint. Let everything dry - it will take a few coats to cover them fully.
Once your pots are dry, use a smaller brush to paint the edges of the pots with white. Let all of your pots dry.
Use the E-6000 to glue the largest pot in the center of the largest clay pot tray. Place a bead of E-6000 around the top edge of the pot and place top down into the center of the tray; let dry.
Place a bead of E-6000 around the inner edge of the next largest pot. Stack it onto the base of the largest pot and let dry.
Repeat with a third pot and let dry. Then glue the small clay pot tray onto the top of the structure. Glue the smallest clay pot as you did the others, on top of the clay pot tray.
Paint the window squares with white paint and a smaller brush. Let dry.
For the window outline, use either Sharpie or black paint and a detail brush.
Video
Notes
Let your clay pot lighthouse dry fully and seal with Outdoor Mod Podge if desired.