It's personal preference. Using hops bags are fine. How I like to do partial mash and specialty grain beers is to use a BIAB bag (boil in the bag). They're a large mesh bag that can usually fit in a 5 gallon pot. I put it in the pot with the water, open it up and use metal file clips to clip it to the sides of the pot. Anything that goes into the bag will be strained out when I lift the bag out of the wort at the end. It makes adding hops and specialty grains a breeze. I just toss them in and then remove the bag after the wort cools down in an ice bath.
Beer so good, it's frightening.
2014: Seven Heavens Series One: Vilon, Mystic Melomel, Skeeter Pee.