When I ordered a bunch of Arduino Pro Mini clones I didn't notice that these don't come with an integrated USB-to-Serial adapter (in fact I needed Arduino Nano - well, I was relative new into this).

So to get a change to use them I've also ordered a CP2102 board that converts between USB and TTL. Since it took a while for me to figure out how to use that I will document it here.

First, connect the CP2102 with the Arduino:

*) Optional, only if the Arduino isn't powered from another source
**) Optional, worked for me without connecting CTS to GND

Next, select the correct configuration.

Arduino IDE

Board: "Arduino Pro or Pro Mini"
Processor: "ATmega328 (5V, 16MHz)" (or the one that is soldered on your board)
Port: /dev/ttyUSB0 (or whatever port the CP2101 is connected to)
Programmer: "ArduinoISP"

Eclipse

Board: "Arduino Pro or Pro Mini"
Processor: "ATmega328 (5V, 16MHz)" (or the one that is soldered on your board)
Port: /dev/ttyUSB0 (or whatever port the CP2101 is connected to)
Upload Protocol: "Default"

Command Line

avrdude -C/etc/avrdude.conf -patmega328p -carduino -P/dev/ttyUSB0 -b57600 -D -Uflash:w:PATH_TO_HEXFILE:i