You can't make sure if the problem is on mo/bo or cpu without checking the cpu on another system, or the system with another cpu. also since i know there is nothing (equipment) to check the cpu if is ok.
About that: "One last thing I do not really get is that if the motherboard was dead then why do things plugged into it still work?" Motherboard has many circuits that working separetly, or according the voltage on other spots (on other circuits). Some could be ok if are stand alone circuits, some might will not functioning because of harm on other spots.