So what you see here is Schematic and PCB and example Arduino sketch of clock implementation with external RTC module. There are also Gerber files for Seeedstudio Fusion PCB service so you can easily produce PCB only for 5$ (not including shipping)
Generally PCB can be used with common anode 7 segment display as well as with common cathode 7 segment display. You only will need to use right type of transistors and connect J5 jumper accordingly.
I did mistake with buttons location. Actually I wanted them at the bottom. Anyway I will do additional version of PCB with buttons located at the right side of 7 segment displays.
I am not providing explanations other then schematic and example of code currently because I don't sure if anyone will be interested. But I will add explanation on request.