For pepakura it can't be done. The reason for that is because if you input a number in either box, whether it be height, width, or depth, the pepakura program automatically adjusts the other 2 boxes. Basically it scales the model as a whole. Although, what your trying to accomplish can be done in a modeler, but your limited to scale the model based on the three axis that are available which would be x,y, and z. But to further manipulate the scaling you can rotate the model. The only problem with doing this, when it comes to scaling the model on a certain axis,(essentially stretching the model) it will cause some distortion to the model, depending upon how much you stretch it.
Another thing to, is you will need to redo the unfold of the model.