Programming the Arduino UNO chips with hex and eep files

Heya all,

I picked up an UNO yesterday and I'm trying to make a project called Ardwiino on Github (GitHub - sanjay900/Ardwiino: Firmware for using various microcontrollers as controllers). There are four files that I need to flash/program: the main hex and eep files and the USB hex and eep files.

As I'm new to tinkering with Arduinos, I have no idea how to use these files correctly. All the guides I found only use the hex file.

For the main chip I found this tutorial: Flashing a HEX file into an AVR / ATMEGA procesosor using Atmel Studio 7 and Atmel ICE - YouTube
He talks something about having a physical programmer. Do I have to get one or can I somehow use the "Arduino as ISP" programmer in Arduino IDE? Secondly, at 0:57 in the video you can see the programmer UI. Under the "Flash" section, where the hex file is used, is a EEPROM section. Is this where I would use the eep file?

For the USB chip I found this: ARDUINO- Upgrading USB FIRMWARE using FLIP - YouTube
At 8:21 after selecting the hex file, there is option to "Select EEPROM". Is this where I would choose the eep file?

I also found this thread in the forums: arduino isp upload hex , eep file - Microcontrollers - Arduino Forum
If I understood correctly it only got so far as to set the fuses? I'm not sure if this is even something I need to do.

I tried contacting the author of the project regarding something else but he/she has not responded yet. I don't want to bombard his/her inbox with my questions before they get back to me so I decided to ask for help here.

Thanks a ton in advance!

Writing the eep file to the main chip (the 328p) requires an isp programmer. The uno bootloader doesnt support writing to eeprom through it. Arduino as isp can be used for this.

For the 16u2, I think you can upload the eep files with FLIP via the dfu bootloader.

I dont watch video, so cant comment on the gui program hes using, but I havent seen a gui tool for uploading via arduino as isp. You can do it easily enough from the command line though.

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The programmer being using is the Atmel-ICE (a $129 professional tool) and GUI being used is Atmel Studio 7.

The actual program appears to be a kludge of Dean Camera’s LUFA controller and who knows what else. I don’t see any usable hex files to load without building with the makefile provided. The GitHub readme markdown file is useless with respect for how to build the software. Sigh.