A passive humbucker gives you the largest playing area and helps tame the extra treble of the EBow. A humbucker also provides two HotSpots for different tones. A single coil pickup has a slightly smaller playing area and a thinner tone. It may require rolling off some highs. The same can be true of active pickups which also might sound better with their volumes lowered to about half.
With two or more pickups on, the tone changes and the volume of the EBow sound is reduced, bringing it closer to that of your picking volume. Also, you can play over one pickup and then the other for two different sounds. For the least noise when crossing strings, play over the HotSpot with just one pickup on.