Those HATs and shields are connected to the main board. It’s completely up to you how to call them. Shield may refer to EMI/EMS shield so it may be confusing. Stack may refer to the layer stackup, so it may be confusing, too. We just adopted “shield” because I remembered it was used with arduino. We have a main device and then different shields. Some are attached to top, some to bottom, and they may be of different size and shape. The problem with “stacked” is this: what you call the added board and the main board? “Stacked”? If you have only one possible stack in mind it doesn’t matter, they may be “bottom board” and “top board”.
As Rene said, you can use a custom footprint for the main board. Even then there are many ways to do it: use one symbol for the whole board and add all connectors as pads to the footprint, or just draw the outline and connector locations as graphics and put the connectors as separate symbols and footprints to the “shield”.
By the way, if you have any doubts about space restrictions in Z axis or other physical compatibility, use FreeCAD and StepUp and create a 3D model for the board which is complete. Attach that model to the footprint which represents that board.
Here is a shield alone and with the main board as a footprint/3D model. The footprint doesn’t have any pads, the connections (pin headers) were added as separate footprints. The actual product won’t have pin headers on the top.