What you’re describing is a “mezzanine” or “daughterboard”, and it’s a very common (but not simple) scenario these days. This thread discusses some useful techniques:
I’m in the process of doing a layout which will have a stacked mezzanine daughter board on top of the main board I’m laying out. It will use standard 0.1" vertical unshrouded headers. So alignment of all the connector through holes is nessesary. This is a multi page schematic with extensive use of hierarchical sheets and global labels to partition the design within the same project.
I have two separate schematic symbols with corresponding related footprints created for Main board and Daughterbo…