The Werhner Way:
Make the ship, add the engine glow (volumetric flames for me), set the engine glow to perfect black, with 0 light produced and no shadows cast (both are options I can set with my renderer). Render the image; it should look like the ship when no engines are firing in Nova. Spin it. Now you have the base.
Next, make the ship perfectly black, with 0 reflection and transparency. Set the engine glows to their appropriate color (orange-red for me). Keep the light emitted at 0 and let no shadows be cast. Render the image. It should look like little points of light with no sign of the ship itself showing up. Spin the image. If you have any inclination of the camera (looking at the ship other than straight down), the flames might change shape as parts are eclipsed by the black body of the ship. Again, I think it is imperative that the ship never is seen, or else strange artifacts will appear in Nova when the ship's engines engage.
Shield glows and weapon glows work the same way. The point is to only show the desired elements to the camera when they are to be shown. Don't show engine glow when you are doing the base, and don't show base when you are doing the engine glow.