Ok let's just start over.
First you need a board with a working atmega.
Then there are 2 steps. 1- Put the boot loader on the chip (this might be done already) 2. Put the sketch on the chip.
To do the first part, load the Use Arduino as ISP sketch to the chip on the board.
Make sure you ave selected the right board and the right port.
Then connect you breadboard like this (bottom secion of this page) Circuit (targeting an AVR on a breadboard) http://arduino.cc/en/Tutorial/ArduinoISP
Like I said it only worked if I used an external clock. (I have the Uno board, with optiboot)
Then use the burn bootloader with arduino as ISP.
Now your new chip as a bootloader!
Then remove the chip from your board.
You could just pop the new chip on the board and program any sketch you would like on it.
But is you want leave the chip on the breadboard and load a sketch on in.........do this.....
Disconnect wires to header pin 10,11,12,13 and connect pins rx and tx the the rx and tx pins on the atmega on the breadboard. Like this http://arduino.cc/en/Tutorial/ArduinoToBreadboard
Uploading Using an Arduino Board
Then add a wire from the board socket pin 1 (reset) to the breadboard chip pin 1 (reset)
Then load the sketch you want to the chip on the breadboard.
Remember never to change the board selection............but like I said it only worked with an external clock.
All this with my Uno board.
So now you can load the bootloader and sketches yourself.