Yes, you're grasping the limitation of complex profiled walls: there is only one vertical stretch zone. In your last/question post, you were still using the word 'composite' where you meant CP. As I understand it, you're talking about CP walls everywhere here.
So, you'd like various heights of stone, a stone sill, and then various heights of wood siding above...
While there are lots of ways to model this, how to do so most quickly/efficiently depends on where/how many doors/windows are being inserted - where I assume only doors will cut through the stone and stone sill as well as the wood siding? And... if you are doing energy analysis, since you have to do more manual work to get energy analysis out of a CP wall vs a composite wall.
A few ways:
If the wall is a frame wall and the stone is a veneer as you state, then the most efficient way of doing this is probably with a composite wall (for the frame wall - gyp, studs/insul, plywood) and using a Wall Accessory. The Wall Accessory is a Goodie that is installed via the Help Menu (Downloads). You select a wall first, then select Wall Accessory from the menus (after the add-on is installed), and define the thickness/material for the stone, the size of the sill, and the material for your siding. This is associated with your wall (although it is a separate object), and windows/doors will automatically cut through both it and your wall when placed in the wall.
See:
http://www.archicadwiki.com/WallAccessories
which is for 15, but the same in all versions... In the screenshot for "Choose Wall Accessory Object" there, it is the "Moldings and Panels" accessory that you'd choose (vs the Wall Framing in the example on that page).
Alternatively, you can do the stone up to the sill as one profile (e.g.), and the frame wall with siding above as a composite. Size each as needed and stack them. For any doors/windows that span both walls, you'll have to place an Empty Opening in the wall that isn't the host of the door/window.
If the face of the stone is not in the same vertical plane as the face of the siding, then getting your trim to appear properly will be the deciding factor on how to insert your windows/doors with any of these suggestions. Depends on if the trim extends beyond the stone, the stone abuts the trim, etc.
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