I'm currently trying to leave the Arduino board aside and starting to program microcontrollers on PCB boards via programming pins. I'm using an ATMega328U from this premade board.
For starters, I'm trying to upload the bootloader. I know every single connection is in place since this PCB is a kit, the FTDI driver is installed on my machine, the cable has been verified to work by using this guide

FTDI Board pins

However I have no idea of how to actually write the program and upload it to the microcontroller. I have been messing with the Arduino IDE all day. My FTDI cable is at COM10, however no programmer available in the Arduino IDE seems to work with this cable, I have been looking and trying all day with no luck.
How can I write code in C and upload it to my microcontroller using the FTDI cable? Do I need specific software to do this? Any special configuration or hack? What am I missing?
Actual schematic of the project I'm trying to program:


I am currently using this datasheet for my cable.


