To program the ATmega1284P, install download AVROSP.
This guide assumes that you have AVROSP added to your PATH.
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When you first plug in the board
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Hold RESET and SW0
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Let go of RESET
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Let go of SW0
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In the terminal, enter the command "mode comx baud=57600 parity=n data=8". Replace the "x" in "comx" with the COM port that your board is plugged into. This can be found in the "Device Manager" on windows (AVR only supports COM ports 1-8)
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In the folder where your .hex file is, run the following command: "AVROSP -dATmega1284P -cCOMx -pf -vf -if "filename.hex" -e".
Install Atmel Studio 7
From fresh code: Download TH3D Firmware https://www.th3dstudio.com/knowledgebase/th3d-unified-firmware-package/ Unzip into a folder of your choice, now referred to as "%TH3D DIRECTORY%"
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New -> Project -> Create Project From Arduino Sketch
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Create a new folder somewhere and select it
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Sketch File:"%TH3D DIRECTORY%\TH3DUF_R2\Firmware\TH3DUF_R2\TH3DUF_R2.ino"
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Arduino IDE Path: "%TH3D DIRECTORY%\TH3DUF_R2\Windows Arduino"
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To find the Marlin Code: see Arduino Core -> include -> variants