Freeweights are definitely better than most gym machines. Machines allow you to lift heavier because they do a lot of the stabilizing for you, which doesn't give you functional strength or work your stabilizing muscles. These types of machines are good for isolating muscle and working on some muscle imbalances perhaps, but it's not good to use them for the bulk of your workout.
Cable machines are very good as well. They provide safety because there's no risk of the weight falling on you, but they allow your body to do most of the stabilizing, as with free weights. The Bowflex is somewhat like a cable machine: it doesn't stabilize instead of your body, and allows you to work those stabilizing muscles.
I think a combo of freeweights and Bowflex would be good.
To do Cathe on the Bowflex, you pretty much just figure out how to do each move on the Bowflex beforehand (correct positioning, etc.) then when you get to a squat or bicep curl or whatever, you can more easily set up the machine for the move.
