Of course, the Fermi level for the molecular energy levels of up-spin and down-spin are same. Usually, the positions of HOMO and LUMO are determined by the corresponding electron occupations, rather than the sign of energy values (i.e., negative or positive). Only the energy zero is set as the Fermi level, you can find out the positions of HOMO and LUMO by the sign of their respective values. The first eigenvalue of molecular orbitals below the Fermi level corresponds to the HOMO, and the first eigenvalue of molecular orbital above the Fermi level corresponds to the LUMO.