So far you have probably learned about MO with diatomic molecules. I.E. Two of the same atoms, and possibly used the MO diagram to determine the bond order and why certain molecules do not exist/do exist.
The key feature here is that they have all been the same. When you begin to have two different atoms or polyatomic molecules, the MO diagram gets funky. Energy levels begin to cross (say the Pi* is lower then the ?bondingl levels begin to cross). Also when they differ in energies different "levels" will have more character (I.E. one will tend to go into the bonding orbital while the other might go into the anti bonding orbital).
So I would not worry to much, just follow the rules you have been taught, as that is what your instructor will judge you by.