Yup, just yank on the cup holder, and it pops right out. To remove the inner part of the centre console, just get a good grip on it, and pull vertically. Completely removing the centre console is a bit of a pain, so if you can route your wiring by removing one or two screws, that'll make your life a LOT easier!
BTW, why'd you have to run wires from the rear of the vehicle? The connectors for the ice>Link Plus (or CD changer) are beneath the centre console.