This paper is the second part (Part II) of a parametric study of the flow and thermal structure in glass melting furnaces with a throat. The effects of the following parameters are discussed: (i) the batch velocity, (ii) the melting temperature, (iii) the submerged depth of the batch, (iv) the wall heat losses, and (v) the thickness of glass melt containing gas bubbles under the batch. The study indicates that the partially submerged batch and heat losses through the refractories have a strong impact on both the longitudinal and spanwise flow patterns of the molten glass. These physical phenomena must be accounted for if one wants to realistically simulate the natural convection circulation of the molten glass in the bath.