I understand their cargo was rather heavy and required specially outfitted B-29 Superfortress bombers--but this also means that they were to be protected at all costs on their way to the targets.

I've heard the story and read about the mission several times, but I haven't come across how the US command went about planning the route for the planes. This must have included how they ensured the safety of the most critical and highly classified American weapon ever designed.

How did they plan the route, for what reasons, and what else was done to make sure the bombers reached their targets safely?