I have an UNO, with an adafruit motorshield connected. The UNO was connected to the USB, I had two servos connected to a 6v walwart. Just these cobined worked great, no problems. I connected a stepper to the shield and attempted to connect my variable DC supply to the shields EXT PWR terminal, but forgot to remove the jumper. Smoke was visible, and I know thats an Oh S%@# moment.
I hook up the UNO by itself, the ON light lights up, as well as the amber light next to the D13 pin, but usually the TX RX blink just when I hook up the USB, not anymore.
If it repairable, I would greatly appreciate a walk through.
I tried bringing up the serial monitor with that board Coding, and it didnt even register with my computer, I am thinking that it is toast! So if that is the case, would the Atmel still be good?
The problem is that it could be damaged in subtle ways. You could face what appears to be a software bug only to discover that the analog-to-digital convert, for example, has been cooked. As I said, it's a question of time. If you want to spend time on a potentially damaged processor then do. In the best case you will end up with a "working" sacrificial processor. In the worst case it will end up in the trash.
If you do decide to play with the ATmega328P I suggest using something other than a computer (like a powered USB hub) to power it.