It's not really that hard, although rather unintuitive, since the procedure is different for arriving and departing ships. For an arriving ship, you just check the special warp option in the ship's misc section. For departing ships it is rather more complicated; you have to instead make a properly timed special-warpout-name event. It causes a knossos (green) subspace effect to form immediately and the ship moves into it. This event must fire when the ship is present in the mission (otherwise, if it still needs to arrive, it will come out near the knossos) and also when it very close to its warpout point (or the warp effect will form too early and just stay there for a long time until the ship enters it).
Or do you mean that new warp-effect sexp? I used that once many months ago just to try it out and it seemed to work fine back then, but I don't know much about that.
