The heavier layer (i.e., the more dense liquid) is the lower layer, of course, but some organic liquids (e.g., benzene, diethyl ether, ethyl acetate) are lighter than water and some (e.g., chloroform, dichloromethane) are heavier than water, so, depending on the solvents being used, the organic phase might be the upper or the lower layer in the separatory funnel. You could look up the densities of the two liquids to determine which is greater, but sometimes a high concentration of dissolved substances in the aqueous phase can cause it to be more dense than expected and to be found as the lower layer in the separatory funnel, even when extracting with an organic solvent with a density greater than water’s.