Hello all!
Recently I have made an Boarduino clone with ATMega168 to substitute my Arduino Uno (which I want to use for development on other projects). I have burn the bootloader and everything seems ok. The problem is that I can only upload sketches (from Arduino IDE and Eclipse with AVRDude plugin) using the 6pin ISP header.
I'm wondering if it's possible to upload sketches using the Pololu Avr Programmer's USB-TTL function (using only Rx / Tx cables)?
Should work fine. You will have to manually reset the board unless...
I believe the A and B pins can be assigned a function so you may be able to get one of those to work as DTR. Once properly connected to the board you will have autoreset / autoupload.
Thank you! I almost forgot about the A and B pin configuration 
Currently I am having problem with serial communication at all. I have written a simple sketch that blinks LED a prints line to serial line every second just to test the Boarduino configuration. The LED is blinking right but I cannot read anything from serial line (connected Pololu Avr Programmer Rx -> ATMega168 Tx and vice versa).