Others will have better answers, but the short answer is that you can't just use any old ziploc bag. Some outdoor stores have the food-grade ziplocs that Enertia and other food companies use; they're usually about 30 cents apiece.

The idea of cooking in and eating from the bag is a good one; I tried it exclusively for about a year, and have done so off and on lately. However, recently I've been swinging back to boiling water in my Jetboil, turning it off, dumping in the meal, and eating from the pot. It just seems to fit my style better: using the bag, I always seemed to be getting sauce on my hands from dipping down into it, because the bag tended to try to shut. That doesn't happen with a pot. For me, I'd rather clean the pot (easy, when there's no chance of burned-on food) than haul a wet, greasy, and maybe smelly piece of trash (the used bag) around with me.

But that's just me. Get the right kind of bags and give it another try - if you like eating from the bag, that's great!