Hey! I had the same question as you. Today I found the right way to land. Basically you need to be right above the landing spot, almost touching it. I say almost, because you should NOT touch it, as it will think you collided with an object and destroy the helicopter. If you stop in this position, hovering over a deck, your action menu (Mouse wheel click) will show "Secure Helicopter". This will actually land it. And from there you can easily move between a helicopter and a ship.