This sounds like a question for the SPM mailing list, and not the dcm2nii forums. dcm2niix will save the tag PhaseEncodingDirection as specified by the BIDS standard. For an axial scan acquired on a Siemens scanner, one would by default expect an A->P acquisition to report
  PhaseEncodingDirection": "j-",
and a P->A
  PhaseEncodingDirection": "j",

Most will want to ignore this paragraph, but for completeness.... By default dcm2niix will flip the order of rows as written to disk (isFlipY = TRUE). The reason for this is that by default DICOM images are written with rows starting at the top left corner, just like you read English text. In contrast, the NIfTI format origin is the bottom left, with subsequent rows ascending the same way we draw the "y" coordinate in Cartesian graphs (y-positive = up).  This would be reversed if the rows are written to disk in reverse order (the undocumented arguments '-y n' will generate flipped rows, and the conversion will warn you Advanced feature: You are flipping the default order of rows in your image. I would expect someone would only flip this if they are trying to emulate the output of some other tool. Switching the isFlip option changes how the image data is saved to disk, and the corresponding coordinates in the NIfTI header (SForm, QForm), bvecs and BIDS (PhaseEncodingDirection). 

The SPM Fieldmap toolbox predates the BIDS standard. I am not involved in its design and have no insight. You could always run both options and see which does the best job.