Well, first off let me just get on the record that I don't think its a given that the Bulls will make it to the Eastern Conference finals. Even if they get the top seed, I think they have a similar matchup problem with the Magic that the Cavs had 2 years ago. Despite being the better team, I think they would have a really tough time getting past the Magic, due to their lack of guys who can really body up Howard one on one. Noah is a very good defensive player, but he just does not have the lower body strength to keep Howard from getting to his spot in the lane...and when he is allowed to get there, it's over.
But anyways, if the C's were to meet the Bulls, I think the C's would be able to use a similar system to what they have used on Lebron and Wade in the past to frustrate Derek Rose. Shadow him with a big man, taking away penetration, daring him to make crosscourt passes, and get up underneath him with his man (who can do that because he has help from the big men), so that if he takes jumpers, he is not able to step in to the shot.
Their only other real threats offensively are Boozer and Deng, but with Deng they really just have to be running him off the shots, because he is not great off the dribble, and with Boozer, they just have to be strong with their rotations on the back side, and make sure they keep him off the boards.
As far as the offense goes, Shaq would be huge in this series, because, much like Howard, he is just a terrible matchup for Noah. If he can get their bigs in foul trouble early, then things could really open up. Beyond that, the defense that Thibs runs (which is the same the C's run), which is great at stopping individual players, is most vulnerable to teams with good ball movement, and lots of balance offensively. If they are crisp with their ball movement, and set good picks, they should be able to beat the defense to get open shots. They also should be able to be effective by hitting the offensive boards, since the defensive scheme can be susceptible to losing guys on the boards, due to how much the bigs are helping on the perimeter. If they move the ball, and force the Bulls to move, then guys like Davis, Krstic, and even Rondo (particularly if they decide to lay off him) could do a lot of damage on those boards.