Re: Can an Ebow screw up pickups?
It should actually go over the 22nd fret, as suggested by the instructions, but really it can be done either way.
If you permanently mounted it over the pickup and let it run continuously, it might cause a problem, but for the minimal use it typically gets, I don't see a problem.
Permanent units like the Sustainiac do suggest keeping it away from other pickups when active, however, and provide an isolation tab for guitars where the middle pickup may be a bit close to the neck driver.
I'm thinking it was designed to work best in older Jackson/Charvels where the middle pickup was closer to the bridge, rather than being equidistant like on a Strat. Either that, or in a 2-pickup H-S which were all the rage when the unit was introduced (George Lynch, Phil Collen, etc)