Am I supposed to use an average modulus in Examine3D?

Examine3D has a single elastic material model so you can only enter one elastic modulus and one Poisson ratio.  The values that you use are up to you.  If the moduli are not too different then an average is fine.  However, if you are interested in deformation in a certain area, you should be using the modulus in this area.  It could be useful to look at deformation using a range of values (spanning from min to max) to get an idea of the influence on deformation and the range of values you might expect.  Generally, in a single material model, modulus and Poisson ratio do not greatly affect the stresses, only the deformation.