CFOperatorU from the Mathematica package

The Crystal Field theory package only allows for a single open shell, i.e. you can not add Coulomb interaction between “non-equivalent” electrons (If I understand your question correctly). The Ligand Field Theory package can handle several open shells and equivalently include Coulomb repulsion between them. In the Mathematica help browser you can have a look at Quanty/tutorial/ligand_field_theory_xas_and_rixs for an example. The basic input is:

XASOppUpd = CIOperatorU[CIBasisXASFull,CIBasisXASFull,1,2,All,All,XASFpd,XASGpd];

for an interaction between shell 1 and 2, including all configurations in the basis.