You Have to Trim your end
Don't be afraid to trim. How often you trim will depend on the length of your transition and the length of hair that you are comfortable with, however, sometimes exceptions need to be made for the betterment of your hair. If your hair is continuously snagging and just all-around tough to deal with, getting rid of some of that relaxed hair can definitely help because it wars against the natural hair that is coming in.
Remember that more important than the health of your natural hair is more important than length. It's good to grasp this concept before becoming fully natural so you won't be holding on to ends that really just need to go.