When I do the character thing, I put referenced characters/pairings in parenthesis. It helps keep it less cluttered and is still pretty easy to understand. I do see your point in wanting to differentiate between referenced characters and main characters, so I think finding some way to do this is important. I would go with the parenthesis, but really, it's up to you. If you're afraid someone might not understand what the parenthesis are you could always do a sample header in a sticky at the top of your journal or in your userinfo, explaining each category and what can be found there.