The best thing I ever did to boost my knowledge about how computers work was to build a simple 8-bit CPU board. One thing that is really different with this setup is that is seems like they are using the Atmega32A as a ROM for the Z80. Seems like an odd choice, but it does make programming quite a bit easier. My own project used an old style EEPROM chip which required a UV eraser to work with..
For anyone doing a project like this to learn about computers, it's worth studying the schematic and paying attention to how the address and data lines interconnect. This will be the basis for how all computers communicate with other components and really cleared up a lot of the 'mystery' for me.