A structure doesn't need to land completely in the influence zone of a structure for it to work, it just needs to touch it.

Open the influence panel (default shortcut - 'X') to show various influence areas while relocating and be precise while landing structures.

You can click the flight slots to select flying structures easier, click the slot twice to go to that structure.

Tap 'A' (default shortcut) to cycle between flying structures.

You can also go to a selected by pressing space, if you hold space the camera will follow the structure.

You can control which way a structure faces when it lands by holding and dragging the mouse when you click on the ground. For buildings this is purely for aesthetics, but it gives turrets a slight edge, because if they face the direction of the enemy's attack, they don't waste time rotating into position.