if there is effective rainfall between two irrigation, from which we hv to subtract that rainfall, whether from fixed amount of irrigation water(5 cm) or from calculated CPE(like 55.55 mm for 0.9 ratio)
The effective rainfall is part of irrigation water to be applied. This is the reason while calculating the water requirement of the crop we add the precipitation to the actual amount of water.
effective rainfall has to be subtracted from water to be applied. If it is known that the temporal pattern of effective rainfall is known in advance (from historical data), then, the other option can be considered. But, as the certainty of the later is not assured by nature, the first option is the practical one among the two.