Jerry and Archie are similar in The Chocolate War because both are individuals who believe in the poster's "Do I Dare Disturb the universe?"Archie gets Jerry to refuse selling chocolates at first because he, too, is "disturbing the universe."
Archie is a leader of the vigils who is isolated almost as much as Jerry is. Archie has Obie and Carter who keep him in check and Archie feels the loneliness at the top of the leadership pyramid. Jerry is isolated from the other students and also from his former friends. In one instance in the novel, the students part for Jerry almost as if he's infected with some illness or something.
What is different about the two of them is that one is the leader of a secret organization and the other is not. Archie also knows how to be political and bend the rules when he wants to get something. Also, Archie has far less of a moral compass than Jerry does. Jerry is honest, as moral as a pure knight, and Archie is not.