The provision of this Chapter, insofar as they apply to employees in the negotiating units established pursuant to article 14 of the Civil Service Law and their dependents, shall be continued; provided, however, that during period of time when there is in effect an agreement between the State and an employee organization reached pursuant to the provisions of said article 14, the provisions of such agreement and the provisions of the agreement are different from the provisions of this Chapter, the provisions of the agreement shall be controlling. The Comptroller may, upon certification by the Director of Employee Relations, provide for the supplementation of benefits provided hereinabove for officers and employees not in a negotiating unit within the meaning of article 14 of the Civil Service Law.