I managed to accidently order an arduino with a surface mount chip. Is it still possible to program/bootload an external atmega328 chip with this arduino? From what I've read it should bootload fine, however, to program it required removing the chip from the arduino itself.
No, there is no need to remove the chip from the arduino board, just load and run the arduino as ISP sketch. Then wire to your standalone target chip. You will most likely have to disable the auto-reset function using a resistor or cap trick.