Aimmee,
Yes, the check would be the same as for a Flat Plate or a Flat Slab but based on the overall depth.
If punching reinforcement is needed, I would think you could include the flexural shear reinforcement on the faces where it is required for the extent of the punching perimeter in your calculation of the area of punching reinforcement to add. Your flexural shear reinforcement will be full width of the beam but you should only consider that which is in the punching zone.
Another solution, if the concrete shape is not fixed, would be to add a Drop panel to the soffit of the beam at the support (as you would do for a Flat Slab but only for the width of the beam, not L/3). This would have several effects for you, reducing flexural reinforcement, increasing flexural and punching shear capacity and reducing deflections. THis would be preferrable as detailing punching shear reinforcement will not be easy.