I’m not surprised at all this feels complicated. After all, this involves symbols, footprints, 3D models and two boards. Additionally, the relation of the two boards isn’t necessarily clear in general case. If there are only two boards, how to call them and which one is actually the more “basic” one? The bigger one, or the one having more powerful MCU controller, or the one which has been designed first, or the one which is attached to different kinds of boards or to which different kinds of boards can be attached? Which one actually defines the physical connection? In this case it looks clear enough, though. But because the OP doesn’t know how exactly to ask, even the seasoned KiCad users confuse the actual problem – and I don’t still know what the OP needs to know.
First, we have a board which already has the connector and the mounting hole (B1). The connector and the hole are there as footprints. If I have interpreted correctly, the OP needs to have those same connector and mounting hole pads in the same location in another board (B2). At least that’s how I interpret the question,
I don’t see a mention of a 3D model there, and the question of a symbol is brought up later.
There are two options for this, and those two answers have already been given. Which option is better depends on several details. Do you want to possibly reuse the B1 in several projects? Do you need a 3D model for the combination? Which one comes to top, which one to bottom?
If you ever need only this one B2, it may be enough to have two projects side by side opened in different KiCad instances and copy the connector and mounting hole footprints from B1 and paste them into B2.
If you want a reusable B1, it would be better to make a footprint which represents it and which can be used in other projects. This has also been described: copy the needed footprints and edge cuts from B1 and paste it to a footprint in the footprint editor. Then add that footprint to B2. If you need 3D model to see the combination, export B1 as a STEP model and attach it to the new footprint.
For creating the schematic for B2 you need a symbol or symbols which represent B1. That should be straightforward because there’s only one connector in B1 for this connection. Even a standard KiCad connector_generic symbol with correct amount of pins is enough. Attach the new footprint to it, and remember that the symbol pin numbers and the footprint pad numbers must correspond.
So, you first should understand your own needs better and communicate them to us better. Then we can tell which solution is the best, and how to continue with details.