I am using an AVRISP mkii.
avrdude: verification error, first mismatch at byte 0x0000 0xcf != 0x0favrdude: verification error; content mismatch
No a program written to work with a bootloader needs the bootloader to work. A program written to work without a bootloader will not (most likely) work with it.
avrdude -c avrispv2 -p m2560 -v