Programming an Arduino using the serial port
Generally the Tools > Programmer selection is only used for Tools > Burn Bootloader and Sketch > Upload Using Programmer and is not used for standard uploads.
For standard uploads you can set Tools > Programmer to anything you like because it will have no effect.
Using an Arduino UNO for serial port programming other Arduino IC’s
A nice and simple way to do it as the UNO has a removable ATmega and the reset pin as well as the UART TX and RX pins.
Remove the ATmega from the UNO.
Connect as follows:
|UNO Pin||Device Being Programmed|
|IO0||RX (programmer TX)|
|IO1||TX (programmer RX)|
Note UNO marked RX pin is uC RX even though the PCB arrow is confusing (it is not connected other device RX)
Using a FTDI cable for serial port programming
Works fine but you need a to implement the reset of the microcontroller. Its often simpler just to use an Arduino UNO (for 5V parts) with the microcontroller removed and connect the GND, RESET, TX and RX pins, like here.
Connect the FTDI cable DTR via 100nF capacitor to to the arduino microcontroller reset pin.
You can pull reset to GND yourself, say using a button on your PCB or the reset button on an Arduino board. There’s a nack of when to release it, its a bit of a bodgit solution, but it can work fine. Releasing as soon as the Arduino IDE says “Uploading” can work, with maybe another press needed once it says “Done uploading” to make the program run.
If the Arduino microcontroller is not reset when trying to program you’ll likely get an error message like this:
avrdude: stk500v2_ReceiveMessage(): timeout