Dear Shachar,
FCI is basically operative, yes. If the Job_Type is set to 'FCI', either standard "Full CI" or Bose-Hubbard Hamiltonians can be treated.
What orbitals will be taken, depends on the input variable "Guess". If you set Guess to 'HAND', then the routine source/ini_guess_pot/Get_Initial_Orbitals.F will be executed to specify the orbitals of the initial guess, if Guess='BINR' ('DATA'), the program will restart with the orbitals in the PSI_bin file ( ASCII file with the filename you specified by Restart_Orbital_FileName) in the working directory.
After the initial guess' orbitals and coefficients are determined, a full CI computation is done -- that is, the coefficients are propagated in real or imaginary time.
Did that resolve your question?
Regards,
Axel