It's actually pretty easy to figure out which gravity well corresponds to the planet you want. The relative orientations of the planets in hyperspace are the same as in the system, so if you open the system map and find your planet is at 3oclock relative to the star, the gravity well will also be at 3oclock in hyperspace. The relative distance from the star is also proportional so the furthest out planet will be the furthest out gravity well. For systems you go to regularly, you can remember which gravity well is the correct one, but you can always check with the system map to guarantee the right gravity well.