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This is really simplifying it but the Commander Amphibious Task Force (CATF) is responsible for sea control and assigning the designated operational areas as well as wave assignments and all that. They would work with the Commander Landing Force (CLF) using liaisons in combat cargo and logistics to figure out exactly what order they want troops and equipment to land on the beach. The rank and position of the CATF and CLF depends on the size of the force. Nowadays, it’s a Navy Captain and a Marine Colonel since they deploy as ARG/MEUs. However, for this operation, they would most likely have been flag officers (I should know my history better). Also, they designate control of smaller elements to other ships. Different ships might be the control for different types of landing craft. That way, the CATF has more of a handle on the bigger picture.
CATF’s staff also gets inputs from each of the different units (ships) and subordinate staffs in the task force to ensure there are no conflicts or special requirements. It all gets put together into a giant timeline and plan which is then promulgated out to the task force in an order called an OPTASK AMPHIB. In order to minimize having to radio back and forth (and there’s a lot of chatter back and forth), everybody has to know the plan and stick to the timetable. They definitely used signal flags and lights and all that to communicate as well as radio. They still do to some extent.
Interesting example: you can hear “CATF, CATF” being called on the radio by Tom Hanks’ character in Saving Private Ryan. It’s when they first land on the beach and he keeps passing info to an R/T operator only to see that the talker’s face is blown off. He calls the guy “shore party” because that is the advanced element which basically handles traffic on the beach. They are the hand-off between CATF and CLF. It needed to be clearly delineated because before it was written down on paper, the commander of the ships and the commander of the landing troops probably argued a lot about where their responsibilities overlapped. Video: http://youtu.be/1pcbPGENImg
This is only roughly how things are done now and I’m leaving out a lot of details. But the SOP for amphib ops hasn’t changed that much since WWII.
**TLDR** – Commander Amphibious Task Force (CATF) comes up with a plan so nobody crashes into each other.
Edit: Saving Private Ryan example and TLDR