The dicom filenames are not part of the standard, so I presume with the filenames you refer to
RP.dcm RTPLAN modality
RD.dcm RTDOSE
RS.dcm RTSTRUCT
flair will convert the RTPLAN to multiple SPOTBEAM, SPOTPOS cards with the proper energy position and direction. If you need a custom energy spread you need to define a beam model in the RTPlan page of flair.
BEAMPOS would be irrelevant, however you need to put a BEAM card to define the max energy of the problem
The rectangular profile can be defined with the SPOTPOS.
Please verify in flair if the automatically created SPOTPOS contain a rectangular profile and not a Guassian.
If you need a custom energy spectrum per spot, this is not possible through the SPOTBEAM/POS cards you would need a custom source.f routine.
You would need to make the geometry of the accelerator head, collimator, MLC manually. As far as I am aware this information is not stored in a standard way inside the dicom files. Therefore flair has no way of creating them automatically.
Yes, flair will correctly create the SPOTBEAM/POS cards as they are defined in the RTPLAN but not the MLC (multi-leaf collimator).
You will need to model it manually.