It depends on the type of element (triangular prisms, cubes, etc) and which way the flow goes to or from the boundary. Assuming triangular prisms, three nodes are needed to simulate flow through the top or bottom of the element, and you set the stage at all three nodes (each stage can be different). For the same type of element but lateral flow across one of its vertical faces, you must set the stage at four nodes, two at its top and two at its bottom. Also note that you must also set the transfer rate at all the elements that share each 3rd type node (the default for all elements is zero). The value of rate depends on the hydrogeology.
Pete