For programming a blank ATmega644, please check this thread:
https://opensprinkler.com/forums/topic/question-about-blank-atmega644-programming/
In short, a blank ATmega644 does not have a bootloader, and hence you will need to program the bootloader to ATmega644 first (through the 2×3 ISP headers, using an ISP programmer such as USBasp or USBtiny). This is necessary if you want to upload a program through OpenSprinkler’s USB port. On the other hand, if you already have an ISP programmer, you can directly upload the firmware to the microcontroller without going through OpenSprinklers USB port.