Just as a point of reference, our design has one large main board and one daughterboard. The daughterboard will likely go away in the near future, but may eventually evolve into various other daughterboards with different functionalities depending on customer requirements.
We are currently treating the two as different schematic projects. Unlike the design mentioned, there is not a one-to-one relationship between the two. In fact, it may make more sense to do the daughterboard and prototype boards, given we may limit that design to only three or less. The two boards are bound together in two different ways: The electrical interface is captured in a 2x20 breakaway header, and the mechanical layout is captured in a 3D SolidWorks model. No truly high frequency signals will pass to the daughterboard, though a SPI bus may operate at a few MHz. Regards, a+
