How they work is you select some ships in one gravwell with a phase stabilizer, and you right-click a second, different gravwell with a phase stabilizer in it. Your ships will then proceed to the edge of the first gravwell that is closest to the second phase stabilizer and fly to it, even though there is no visible "phase lane" between the start and finish. You don't have to select the phase stabilizer or move closer to it or anything - that's all handled automagically.
Some notes:
- Phase stabilizers must be 100% completely constructed before you can fly between them.
- No antimatter is consumed.
- Various upgrades can really speed up your passage while in phase space.
-- Retro