Bullpen usage is an issue that persists even in v6.5. The patterns and degree of usage, based on your bullpen order on the pitching staff screen, don't always make a whole lot of sense. There's no significant problem with putting a guy in two relief spots. In fact, it's common to make your closer both the closer and one of the setup men to ensure he gets enough innings.
I've always played it as if the order is the order in which you want them to be inserted into the game (1st middle if available, then 2nd, then 3rd, and so on). I can't tell that this is strictly followed or not when simming games, personally, but it seems to generally balance out the innings okay.
Not much help, I'm afraid, but know that you're not the only one confused.
