When you describe the skin-stringer concept with spars, I assume that you are describing skins with relatively small stiffeners and then fairly large beams for spars. If that is the case, the preferred modeling approach is to model the skin-stringers with plate elements and then model the spars as beam elements in your finite element model.
Then when you import the model, the skin-stringers will come in as panel components in HyperSizer and the spars will come in a beam components in HyperSizer and you can size each according to the loads in the FEA.
Alternatively, if you have full depth spars (i.e. full wing depth), then you could model them with plate elements and then you would have separate panel components representing the skin and the internal structures. Both modeling methods are effective.
If you look at the wing structure in the AP1 training model described in the Pro manual, you will see this type of modeling where the skin-stringers are represented as one panel component and the internal structure ribs and spars, which are full depth, are represented as another panel component.