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Most dishwashers, when started in a normal wash cycle open the cup in the first wash cycle. So if you add detergent to the prewash and the main wash cup your are basicly over dosing Your dishawasher with detergent, which can lead too performance issues and even damage to Your dishwasher.
When dishwasher is set to normal wash the only reason why you would want to use the dispenser to release detergent would be if You are using a liquid detergent. Due to the fact that most dishwashers will drain before they fill You have a chance of wasting the detergent You put in Your dishwasher.
By only putting detergent in the prewash you are only chancing the loss of your soap if the dishwasher drains before it fills. There are no other benefits or consequence to putting the soap in just one cup or the other on a normal wash.
During a Pots and Pans/Heavy Duty cycle you would be losing the benefits of the second wash by not adding detergent to both cups.