Starting with a typical Vintage Stratocaster the coil is wound Top Left/ Top Going. If you look at a top view of a stock Fender Stratocaster pickup, eyelet’s at 6:00 O’Clock and the cover removed you will see the beginning coil wire starting on the lower left eyelet and the coil winds clock wise around the bobbin and finishes on the lower right eyelet. If two or more coils are wound in the same direction with the same magnetic field they will be in phase. If one coil is wound Top Left/ Top Going (counter-clock wise) and the other coil is wound Top Left/ Top Coming (clock wise) with the same magnetic field the two coils will be out of phase. If one coil is wound clock wise and the other is counter-clock wise with two opposite magnetic fields the pickups will be in phase and humbucking.

I would keep the coils wound in the same direction if you don’t have any means of re-magnetizing the pickups. If the pickups you are using have two different magnetic fields (after market pickups) then it would be best to wind in opposite directions.