I've done the 2x4 wrapped in beach towels trick before, and it works well. But, the OP is talking about designing (or redesigning) a real double stack trailer.

One other thing to consider is flexibility in the design to accommodate a third boat. Not something that's done every day, but gives you the option to buy a new boat, help with a sale delivery, get another boat to a big regatta, etc. Sort of like us with the single trailers jury rigging up a double stack, you could plan ahead to turn your double into a triple on demand.

Mike