Are the characters listed in any specific order? If so, what is it?
I assume you mean the characters on the character list provided in the Enotes Study Guide. Owen Meany is listed first, likely because he and the narrator are the protagonists of the novel. The rest of the characters are listed in alphabetical order by their last names, or the only name provided.
The more primary characters in the book of course have the lengthiest descriptions, but as far as rating the importance of the minor characters, the Enotes list really does not attempt to do this. One way to track important characters as you read is to keep a list of those who recur in each section of the novel. Those characters which play a role throughout Johnny's (and Owen's) growing up tend to make more meaningful impressions. Think about characters such as Tabby (even though she dies, her presence/absense is still a big deal throughout the book), Dan, and of course, Hester.