My opinion, which you've probably seen on here if you've done any looking around before deciding on the MC2100 or how to install it, keep as many of the hoses as you can.
I have a thread where I went through with the rear valves and the MC2150 and connected just about every line I could. Granted, I don't have the OEM smog control on the manifolds or the stock air cleaner, so it's a lot less messy, but here's my thread: http://www.jeepforum.com/forum/f8/ca...-help-1064615/
I'm picking up an MC with the bowl vent soon, so I'll add that line to the list of things to connect to the canister. I think once you understand where everything is going and why, it seems a lot less messy.