Vortices and vortex arrays have been used as a hallmark of superfluidity in rotated, ultracold Fermi gases. These superfluids can be described in terms of an effective field theory for a macroscopic wave function representing the field of condensed pairs, analogous to the Ginzburg-Landau theory for superconductors. Here we establish how rotation modifies this effective field theory, by rederiving it starting from the action of Fermi gas in the rotating frame of reference. The rotation leads to the appearance of an effective vector potential, and the coupling strength of this vector potential to the macroscopic wave function depends on the interaction strength between the fermions, due to a renormalization of the pair effective mass in the effective field theory. The mass renormalization derived here is in agreement with results of functional renormalization-group theory. In the extreme Bose-Einstein condensate regime, the pair effective mass tends to twice the fermion mass, in agreement with the physical picture of a weakly interacting Bose gas of molecular pairs. Then we use our macroscopic-wave-function description to study vortices and the critical rotation frequencies to form them. Equilibrium vortex state diagrams are derived and they are in good agreement with available results of the Bogoliubov-de Gennes theory and with experimental data.