AXY and HB refer to the pickup shapes. The AXY is the classic Alembic soapbar size, and is the same shape we use on Series I basses, Spoilers, and Stanley Clarke models. HB are direct replacements for Gibson humbuckers.
The electronics suffix of AE-1 is only for 1-pickup models, like a P/AE-1. That will get you the split P pickup and 1 volume and 1 filter control.
Most of the electronics we sell are the PVF (like AXY/PVF). These include a pan, volume and filter control.
AE-3 is the suffix for the pan-volume-bass-treble arrangement of controls. You can use just about any pickups we make with either the PVF or AE-3 electronics (or even electronics from an offered model, like Signature).