I did my own Mega board, because I needed some Mega2560 pins which are not available on the Arduino Mega.
If you know eagle, then the link from johnwasser is excellent advice. There is a free, limited version of eagle.
I recreated the PCB in KiCad. I used all the parts as specified in
https://content.arduino.cc/assets/MEGA2560_Rev3e_sch.pdfSome things to be aware of:
- The atmega2560 chip is only available as SMD. So you will have to solder SMD, or get it done at some PCB manufacturing place. I use elecrow. (No advertisement intended, just my good experience with them)
- follow the advice in the atmega datasheet about connecting all the Vcc and Gnd Pins, and the blocking capacitors, and positioning of the crystal.
- your microcontroller will not have a bootloader. Include a ISP header on your PCB for burning the bootloader. You can use any arduino to build a bootloader.
- if you plan to use one of the USB-serial adaptors, don't forget the capacitor in the reset line.
- your first version of the PCB
WILL have errors. Design the PCB in such a way as to facilitate troubleshooting: Expose test points, be generous with headers, don't pick the smallest SMD parts, think about the 5V power supply, include test LEDs, etc.
Good luck
Thomas