Firstly it provides the ability to target an invasion. This can only be done when the Amphib HQ is in a port. Just like with Airborne Ops once you have targetted a hex the preparation points begin to accumulate.
Of course an Amphib HQ is only one element of an invasion force. The invasion force is prepared by stacking units with the Amphib HQ. This means that up to two divisions can accompany each Amphib HQ (ships permitting). However the larger the units, the more of them and the smaller the Port the slower prep points will accumulate. In addition only Commando or Ranger Units and Naval Support Groups can be attached to the Amphib HQ to provide support during the invasion.
When sufficient prep pts have accumulated (50 for Amphib HQ and 30 for Combat Units) you can invade.
The invasion itself takes place automatically once you press the INVADE button on the Amphib HQ counter in the Unit Bar. The invasion itself takes place between your turn and your opponent's. The invasion assault looks to place your combat units in the targeted invasion hex with the Amphib HQ staying in an adjacent sea hex. An attached commandos will look to occupy an empty hex adjacent to the invasion hex. The only support units that take part are those attached to the assault units or the naval support groups attached to the Amphib HQ.
Once ashore your opponent has the chance to drive you back into the sea before you get to establish things further with follow up forces. When you get to your turn you will notice that the Amphib HQ has done three more things: firstly it has created a temporary port to allow you to unload units and freight; secondly it has created a depot to hold and distribute freight and finally created an air base for you to fly in air supporting units.
The screenshot shows Amphib HQ and its co-stacked units ready to invade Omaha from T1 of the 1944 (D-Day Start) Campaign.







