A molex connector has 2 grounds, a 12v line, and a 5v line. Red = 5v, black = ground, and yellow=12v. When measuring voltage, you need to ground the black end and then use the red end to find the voltage. What this does is find the potential difference (aka voltage) from whatever you're touching to the ground. It's very practicle to stick the black end of the multimeter into the black female molex connector to ground it. Then you just need to worry about the other end making contact.

To measure resistance, you need to turn the system off and disconnect power. For the vdroop mod, just measure the original resistance (its 129.5k ohms on the P5N-E) and take it down in 10k ohm steps until you dont have vdroop anymore (smaller incriments as you get closer to near 0 vdroop). Don't worry about how hard or soft to make the marks...just make marks until you get your desired resistance. For vcore, just measure the original resistance and take it down in small incriments until you get your desired vcore raise.

It usually helps a lot to have the system out of a case.