You can move your ship(s) whereever you want by holding down the [SHIFT]-key. A movement marker will appear, which you can move on-screen with your mouse. By also holding down the left mouse key you can move it further away from the camera and back again.
Other objects will display markers as well and if their markers start to blink, then your selected movement marker is roughly at the same distance to the camera as the blinking marker.
It's much easier than it sounds... just somewhat difficult to explain. You'll get used to it rather quickly and although it lacks the precision of the Homeworld system, it suffices for most maneuvers you'll ever want to try.
In case you didn't already know, you can also detach the camera from the current ship by double-clicking on empty space instead of another ship. Then you'll use the mouse wheel to move forward and backward and the right mouse button to rotate the view. This way you're not restricted to follow a specific ship, but can choose your own viewing angle.