How about using eyelets like these?
Caldercraft Fittings Brass Etched Eyelet 0.3mm (250), Model Boat Fittings, Model ship fittings
Thread the eylets first then make a small hole in the appropriate bit of your ship and glue the eylet into the hole with superglue. Then tie off the cord to the right length and glue for strength.
Tip. Use a dab of superglue on the end of the thread and let it dry. This makes a stiff end which is easier to thread through the eyelets.
Just a thought.