checking iPhone with multimeter

What device are you testing?

Your approach is fine...for continuity, it doesn't matter whether the red or black probe is on ground. By convention, it should be the black probe. To find the component that is actually causing the short is a bit more difficult. Any component on the shorted line will also appear shorted. You have to use any visual clues (damaged or corroded components) or intuition (which part of the phone is not working or if the entire phone, where is there the most damage).

Finding a short on a main voltage rail like PP_VCC_MAIN is more difficult as there are dozens and dozens of components which could cause this. Ultimately, you may just have to start pulling components one by one. There are more advanced tricks like injecting voltage and looking for overheated parts (using freeze spray) as well.

Give us more details about which device you are looking at and what the problem is and we can give you more directed help.