The influence of a Co or phthalocyanine (Pc) molecular overlayer on the properties of quantum-well resonances (QWR) in Cu layers atop Co(001) is studied by means of spin-polarized electron reflection. For Co atoms and Pc molecules, an energy shift of the QWR-induced signal is observed with increasing coverage and is attributed to a variation of the electron reflection phase at the Cu/Co and Cu/Pc interface. For Co we find a linear energy shift in the Cu QWR energy position with increasing coverage down to the sub-monolayer regime. This shows that the phase accumulation model remains accurate within the sub-monolayer regime of a discontinuous interface. An opposite sign in the energy shift between Co and Pc overlayers could reflect an opposite impact on the Cu surface work function of overlayer adsorption.