Hi @jonyibandi
There were some very good ideas in this thread where I asked a similar question.
The project I was asking after there is now at the PCB manufacturer so can’t give you the full story on how ite went but can speak to which of those options I did. Mine had two PCBs, one as the main board and the other attached at a right angle which included the controls that would poke through the front of the enclosure. It’s very similar to your idea, but mine are at right angles rather than being a sandwich.
FIrstly, since my two boards each were quite large, I didn’t create the two boards panelised but kept them both to smaller than 100x100mm to keep the manufacturing cost down. In that thread you’ll see some great advice about having one gerber but having the ability to cut it down a row of mousebites in the board to make the two. Yours might suit that but mine did not.
If you want to have two PCBs made and not cut, this is what I did:
I created one schematic and selected footprints for the entire project, then when I opened pcbnew for the first time and imported the netlist, I saved and exited, then copied the .kicad_pcb file so I had two. Then I opened each in pcbnew, and deleted the footprints I didn’t need so there was nothing common between each PCB design. One of these PCBs will be named for the project so will open when you launch pcbnew with the project open. The other will show in the file list as its in the same project directory, and doubleclicking on it will launch pcbnew to edit it.
All in all I was happy with how this process works - the only downside is when I changed the schematic and re-exported the netlist, all the unwanted components reappear in each board but they’re easy enough to delete.
Hope this helps,
Geoff