Hi, Needa.
You apply the Multilayer Well ou Well BC to a certain node. If your model has just 1 layer, you can assign the BC to the last slice if that suits your conceptual model.
But even if you have onde geological layer, it doesn´t obligate you to use just one numerical layer. If you create more numerical layers it will permit you the use the wells whatever slice/position you want.
Hope I have helped you.