Instructables user Inspiredwood has a great tutorial on how to make a conventional ship-in-a-bottle, but he also reveals an interesting tip from his childhood: he used rubber thread to simplify the ship's rigging.
I used to do quite a few bottle ships as a kid. But I'd use rubber thread instead of real sewing thread so I wouldn't have to construct the ship to accommodate the complex rigging necessary to pull up the masts and sails. The rubber thread would do the job by itself once the ship was in the bottle.
The masts will still need to be detached, but the elasticity of rubber thread (like elastic sewing thread) negates the necessity of complex rigging when sliding the boat into the bottle and raising the sails. Instead, the rubber thread can be glued as it will be in the bottle, and then stretched and distorted when inserting the masts with the ship. Essentially, it's self-correcting if properly constructed. Although the rubber might not age well, it's a good tip if the minuscule rigging seems too complex to tackle.
Bottle Ship [Instructables]