2560 With my PCB

Projects General Guidance
2

  1. As far as I know, it is fundamentally the same, except for possible issues with pointer arithmetic.

  2. Yes, I've flashed the bootloader a few times.

  3. You use the same development environment. Some things, like timers, are going to be a bit different if you address the registers directly. Some libraries may not work with it, until you tweak them. They may assume certain pins do certain things (eg. I2C, SPI) and may need adjusting.