The idea of the B747 prototype being a 'double decker' design was clearly an idée fixe of Juan Tripp, Pan Am's then head.
Apparently, the double deck mockup that Boeing presented to Pan Am was a charade, designed not to sell this version of the747, but to kill it. It was clearly a descendant of the Stratocruiser, with two intersecting lobes (the lower one larger, and the upper deck beginning where the lobes met at a seam, roughly 2/3 the way up, similar to an egg in an egg cup) with an upper deck at 25ft of the ground.
When Pan Am's top technicians and Captains were looking at the mockup, the idea of an evac from more than 25' off the ground and the lack of underbelly space for cargo was miserly - especially for an aircraft this size.
'The Boeing engineers had ideas for a different cross section. A single circle, passengers would be 16'off the tarmac, and there would be 9 seats across, with two aisles, and spectacularly wide - about 20'. What the Pan Am techs liked was the underfloor cargo space - there was room for 2 8x8 containers side by side. Juan Trippe had insisted that future cargo would be as important as passengers, and Boeing listened.
The source of this info is from: "Widebody- The Making Of The 747'
Clive Irving
ISBN 0-340-59983-9
A really wonderful read that goes back to Boeings B47/B52/B707 days in devlopment of the swept wing jet aircraft.