But using, for example, the standard "Arduino Uno", it will try to upload via serial to a bootloader. I create entries in boards.txt for ICSP programming, like below. Different programmer but should be same approach with an AVRISP mkII.
m328p16.name=ATmega328P ICSP @ 16MHz
m328p16.upload.using=usbtinyisp
m328p16.upload.maximum_size=32768
m328p16.bootloader.low_fuses=0xff
m328p16.bootloader.high_fuses=0xde
m328p16.bootloader.extended_fuses=0x05
m328p16.build.mcu=atmega328p
m328p16.build.f_cpu=16000000L
m328p16.build.core=arduino
m328p16.build.variant=standard