Hi hope you can help
I will be running my 1280 board using a 9 volt power supply connected to Vin. I note that the 1280 will also draw power from the USB port when it is connected. My question is - will I damage anything if my 9V is connected at the same time as the USB is plugged in?
no, you will not damage your arduino or pc. in some cases, you must connect both, power and usb. ie. if you want tho programm or debug the board and have a lot of load on the board installed witch will exceed the maximum power-rating of an usb-port.