If doing cardio to lose weight, and not for actual cardiovascular endurance, it's best done on an empty stomach right after you wake up. It's tough to do when living a normal life. Also, most people frown upon doing cardio before lifting because of the decrease in strength.
So it creates a problem, do you do cardio on empty stomach, take protein and lift with decreased strength, or take protein, lift, then cardio? I have always done the latter with great success. While running, I sip on a concoction of orange gatorade and vanilla syntha 6. It's a unique flavor. I down whatever is left when I am done running.
Everyone is different, so I wouldn't be surprised if someone disagrees, but like I said, after doing this for 15 years, this is what I have found to work for me.
As you said, cardio first thing in the morning is best, but if you have to do it all during a lifting session, lifting then cario is the way to go. The reason is two-fold. First you get to use your glycogen stores to lift heavier weights, and then once that is depleted with the weight training, your body goes straight to burning fat without having to bur through the glycogen first when you start cardio.
To do it the other way around your body will take longer to get into the fat-burning zone, thus less fat will be processed as fuel, and you'll then have nothing in your muscles to push the weight up with.
As for the OP's question about an empty stomach, I usually don't eat for at least an hour before I lift, but that's not to say that I have an empty stomach when I hit the gym. The goal is to have fuel for your muscles all day long, as if you truly have an empty stomach your body will go into starvation mode, your body will then store fat for the percieved long-term famine, and use muscle for energy.
All the times I have successfully dieted without adversely affecting strength I was never hungry. If you do it right your body will have ample nutrition, and still turn to fat for energy when requested. It may not be as quick as a fad diet, but it's alot healthier, and usually the progress is more long-term.