To upload a program into an ATMEGA328 Chip with Arduino bootloader already in, You need :
1. a USB -TTL board.
2. Connect them right. What is your USB -TTL Adapter ?
Let take the one here : http://www.hvwtech.com/products_view.asp?ProductID=1107
A FTDI breakout USB-TTL adapter.
But first, make sure the Arduino chip is connect right.
1. The Vcc : pin 7 and pin 20. -- + 5 V
2. The GND : pin 8 and pin 22 -- gnd
3. The X-Tal : pin 23 and pin 24 -- 16 MHz Crystal and 2 X 22 pF cap to GND.
To connect the FTDI : For that particular board : RX --- > TX pin 3 TX --- > RX pin 2
And.... Connect the : DTR ---- > 0.1 uF cap -----> Reset pin 1 The cap is in serie.
In the IDE, choose the right USB port number and the right board. The board I choose is : Arduino Pro ( 5 V 16 MHz ) ATMEGA328.
Try it and see what happen...
If you have still problem, a picture of your setup will be nice.