Trying to repair my Arduino UNO board

Any idea if USB interface chips come pre-programmed or how to burn them after installing it. I am not sure if my skills are quite that good either but I will probably give it a shot as I enjoy soldering, if we think that is the mostly next step.

As far as programming it through the ICSP, To test this I am using the default blink program.

Do I still program it with the same setup as when burning the boot loader? I tried this a couple of times, using the Mega to program the UNO. I did see the LED by the L blink presumably when the Mega reset the UNO, after a few seconds I see this message pop up again:

avrdude: stk500_getsync(): not in sync: resp=0x00

I find it odd that I can seemingly upload the boot loader as evident that the reset button works but I cant seem to load programs. Is there an extra step I am missing somewhere?