In your question, it sounds like you've fleshed out several characters. However, it's unclear whether you are using the word "protagonist" in its traditional sense.
Most stories usually have one protagonist. Less frequently, a story has two protagonists. And then, their goals must be closely related. The story revolves around the struggle of the protagonist(s) to achieve her aim. I would avoid tackling stories with multiple protagonists until I was confident of my ability to write great stories with only one.
The other characters in the story should serve only as supporting cast. Their actions help or frustrate the protagonist's progress. Their personalities contrast with that of the protagonist. Their storylines intersect with and sometimes serve as a counterpoint to that of the protagonist.
One "methodology" is to use archetypal characters for your genre. They're archetypal because they possess a nearly ideal set of qualities for a given type of story. Readers may also have an easier time "stepping into" a story that relies on archetypal characters. Your job, as the storyteller, is to use those characters interesting and novel ways.
If you're not sure that a character in one of your stories doing a good job of helping or frustrating the protagonist, consider enhancing the character or removing them from the story. You can reassign their useful qualities/actions/dialog to another character.