You've got to make your mega2560 work with your micros. There's no secret in making it work. Just follow the official tutorial. Did you have a capacitor on your mega as instructed?
My suspicion: you used the bootloader to load your flash image but the bootloader can't write onto itself so the bootloader is lost. The process is to first erase entire flash (code and bootloader both lost) and then write to flash. Because you didn't use the ICSP header but relied on bootloader to write flash, the chip erase succeeded but because it is unable to write to bootloader region, your new chip only had program on and not bootloader. You can only fix your mistake if you manage to get mega to talk to micros and then redo what you did with that command, directed at mega's port. Then micro will be in reset and communicates via the ICSP header, which can write to any flash region.
So get the tutorial working, first maybe with mega and another arduino, such as mega or uno. Then get it working with micro, and redo your flashing. Don't flash with bootloader because bootloader is a program, and unable to write to bootloader region. That's my guess.