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Yes, of course it can be important. Actually, the parasitic capacitances of the plates of a capacitor are different because of the difference between the distances of these plates to the substrate. Usually the plate with the bigger parasitic capacitor (nearer to the substrate) is called as the negative plate. In some applications, these parasitic capacitors may cause difficulties such as in sampling capacitor of a SHA circuit. In these cases, the negative plate usually place at the position with less degrees of importance.