Hi @ejdavid,
I am not a multi-echo expert, but I can partially answer these questions.
As far as I know, fmriprep does not handle b1 fieldmaps, but should be well equipped to handle your PEPOLAR (AP/PA) fieldmaps, of which you should only need one pair (and it will probably throw errors if you try to use multiple). See here for naming rules: Magnetic Resonance Imaging - Brain Imaging Data Structure 1.10.0 . Keep in mind you will need to use either the IntendedFor or B0FieldSource / B0FieldIdentifier method to associate fmaps with your BOLD images (see here: Fmriprep 23.2.0 didn’t do sesceptibility distortion correction - #4 by Steven)
I would use the gradient corrected T1, see here for anatomical naming conventions: Magnetic Resonance Imaging - Brain Imaging Data Structure 1.10.0. I am not a multi-echo expert, but I believe that fmriprep can do something with the multi-echo t2star images. Perhaps someone else can chime in.
For fmap quality assurance, you would check that the distortion correction is actually improving geometric correspondance between anat and BOLD images, which is included in the HTML report at the end.
Best,
Steven