I tried making pudding in the microwave for the first time. I took 20 g rice starch and 250 g milk. First made a slurry, then mixed the rest of the milk, constantly stirring. Then added 10 g sugar and half a tablespoon of vanilla extract, and stirred well again. The mixture was fully homogenous.   I put it immediately in the microwave at a low setting, and turned on for 3 minutes. It was still really liquid, so I put it in for another 3. When I took it out the second time, it had built a skin. I tried stirring it in, and suddenly realized that all the starch has sedimented on the bottom and has half-gelled there. Stirring with a spoon only broke it up into solid pieces.   I blended it smooth, cooked it some more, and got a thin, reasonably smooth pudding. But the question is, how should I have prepared it from the beginning to make it in one go, without a blender? 
I'm not sure if you mean each portion is in a separate bag and then you're placing the entire contents of what you bagged into a heavier plastic bag designed for freezing. If that's what you mean, it's fine but I'd pick up extra unused plastic pull n pak bags so you wouldn't need to worry about cross contamination with used bags. It's what I often do when separating raw meat. It makes it more sanitary for me as I turn the bag inside out, then put it over my hand like a mitten. I grab the meat with my hand in the bag and turn it so the meat's contained in the bag without me having to handle it.  On the other hand, if you're storing the meat in those bags only, I don't suggest it. Other than cross contamination like Alan mentioned, those plastic bags were never meant as a thick enough barrier between food and freezer air and contents. It's easy to get a tiny tear or puncture in the bag and get freezer burn on the meat or the odor of the raw meat to mix with freezer air. You might not notice it at first but over time, your freezer could get a funky smell affecting other food in it.  My aged mother was always freezing meat in these bags and never noticed how off her freezer smelled. She didn't understand why parts of the thawed out meat looked dry, had freezer burn or developed ice crystals in it. I don't say yours would get that bad but don't rely on those bags only.  Nothing wrong with using them to store vegetables in your fridge though. I prefer to wash and dry most of my vegetables when I bring them home. I wrap a paper towel or two loosely around them and put them in the fridge then. 