You can move the ships manually by selecting your ship(s) and holding the SHIFT-key. You'll get a move cursor, which you can move around by dragging the mouse and move back or forward ("into the screen") by left-clicking and dragging the mouse back or forward. Other visible objects will get their own cursor, too, and start blinking when your move cursor is at the same distance as them ... allowing you to better judge the distance of your move order. When you release the SHIFT-key, the selected ship(s) will move to their destination.
Using the same control scheme, but by holding the N-key instead of SHIFT, you can also place your own navpoints in space. This makes it easier to set up staging areas or rendezvous points for your fleet, because your ships can use the standard move commands in combination with these navpoints.
Seems cumbersome at first, but is pretty easy to use. You still can't assign a complex move order, though, where your ships follow a path of multiple waypoints.
Have fun, though. Besides the awkward controls, Nexus is still a great game for sci-fi-fans