Carbs will be first used for energy, second stored as glycogen in the muscles and liver, and only last are they converted to fats - this happens when either muscle glycogen is full, or you've eaten too many carbs in one sitting.
I get carbs from fruits and veggies, and occasionally I will eat some grains, but only AFTER a good workout. I know grains are neither paleo nor all that healthy, but they are just so darn good for insulin response and storing glycogen in muscles. I do eat raw meat about 95% of time.
[personal opinion - carbs, even cooked, tend to remain just carbs. Not really any extra toxins or whatever. Meat however, the fats are so complex, varied, and heat sensitive, they change significantly and create toxins. Thus I see eating cooked carbs as being moderately okay - if done in conjunction with intense workouts - and cooked meat/fats as being a culprit for the slow destruction of the body. Insulin resistance also destroys the body, but intense workouts increase insulin sensitivity so it balances out if you do it right]
If you have messed up digestion, I'm not really sure how all this factors in. I would definitely recommend separating your carbs and protein. If you're looking to put on weight, you might try eating a good amount of carbs (something that doesn't upset your stomach), wait 20-30 mins, and then eat some really fatty meat. That way you can get protein/fat in the body while your insulin levels are still elevated, w/o the problems of protein vs carb digestion.
Also, I guess some people here do really well on ground beef, I do not. It took me a few months of cycling between feeling fine, and diarhea/poor digestion to figure out it was the ground beef. My theory is that since it's already ground into a mush, it passes from the stomach to the intestines without having the full acid/digestive treatment by the stomach. Either way, I haven't had stomach issues since I cut out the ground beef.
One last thing, if you eat fat with carbs, you WILL put on weight, most of it fat. B/c now you have an insulin response which tells your body to store anything in the blood stream, and there is fat in the blood stream.