Cardio on an empty stomach or with a small amount of protein only in the system is supposed to be better for fat burning. However, if you do intense cardio this way, you stand a good risk of catabolizing muscle away. If you have a lot of fat to lose, then low to
moderate intensity cardio i.e. 20-40 minutes of walking at a moderate to fast pace is a good idea.
Personally, I chose to lift in the morning and do cardio in the evening. I feed my cardio workouts just like I feed my weight workouts and use the highest intensity level I'm able to use. However, in my first two years I only managed to burn 160lbs of fat and add 40lbs or so of muscle. End result was a small, weak, 180 pound -ish guy at 6-8% body fat - depending on the way it's calculated. Now I'm back to around 190 with 10-12% BF.
My personal belief on cardio is that it is for improvement of general conditioning, endurance, cardiovascular function, pulmonary function and athletic ability. By improving these things -
weight training gets better. Think about it, how will you perform better - out of breath after 2 or 3 squats or still getting good oxygenation to all your tissues and able to keep going? Fat loss or gain is controlled in the kitchen.