You'll need to fly as close to the object you want as you can, stop, jump to the turret, switch to tractor beam ('w' key) target the little bugger and hit the fire key.
(I think it's like that, or you simply fire it like a missile...'Enter' key)
It's a bit tricky as the cargo keeps flying around (and you need to be careful not to hit them with your ship or they might go BOOM), but the tractor beam should have sufficent range to catch the little buggers even if they managed to get some 3000, 4000 and even 5500 klicks from you.
You'll see a blue beam catch the bugger from above it (??? I never got that...) and it's range should start droping until it gets down to 0 (when it gets into your hold)
You should stop your ship as if you don't and the bugger get out of range (even while tractoring) the beam will disengage and you'll have to start all over again. (I think it's range is around 6500-7000 klicks).
Also, if you fly at a high speed (only the centurion) the cargo might miss your ship (?!) and not get into the hold. in this case it'll keep flying by inertia until the tractor beam get over it and pulls it back in! (or it might even fly off after passing the 7000 klicks range...
). In short - go to a DEAD stop.
An alternative is to give up one of your warhead tubes for a forward mounted tractor beam emitter - in this case, put the cargo on your site, fly toward it down to tractor range and pull the fire button (the MISSILE fire button, not the GUNS...) and thats it.
but for that you loose a missile tube so...
