As you get farther along and build more dexterity and finger strength you'll find that you'll usually want to use the 3-finger approach. It gives you more precision and generally better tone. As you get better you start to really hone in on the tone and dynamic each string produces. Three fingers on power chords let's you adjust those string vibrations independently to shape the overall chord. It's one of the things that makes a more advanced guitarist sound so much better even if you play the exact same thing.

Personally, I like to consider these different techniques as tools. Learn them all. You will find yourself eventually needing every tool in the toolbox rather than learning a single way to shape a chord.

Stick with it and it'll get comfortable. Good luck!