Joel is right. I did mine from the top side, without ever getting under the car, but I did have to cut a rectangle hole in the tunnel towards the passenger side from where the shifter actually comes up through it. I drilled 4 holes where the corners of my cut-out would be and then used a small air-saw to cut the rest out. After I was done, I cut a piece of sheet metal a little bigger than the hole, and used 4 rivets (plus gasket maker all the way around) to close it back up.
+1 on going ahead and having a new shifter boot while you do it. The stock one is probably torn and you might as well replace it while you're in there. Before changing the shifter, I could feel hot air coming out of the tunnel and into the car form the shifter area. Completely gone now.
I would agree that doing it from under the car is probably the way to do it, but my way worked out fine and I was tired of being under car doing my winter clean-up. Plus, I have become way too comfortable cutting on the Viper after installing the roll bar.