Is cooking with whole grain flours the same as eating whole grains?

I read the other day that it is healthier to eat whole grains and to avoid processed grains, but then I saw on the internet folks who sell 'whole grain flour' and I became very confused. Please help. I ask this because I'm seeing signs in my health that tell me I'm headed toward diabetes, but can still pull out before its too late. Thus the advice to eat whole grains. I'm gluten intolerant, so I already do my own cooking, but I do utilize flours to make pancakes, etc. and am currently going off sugar, which is very hard to do. Any advice is useful. Thanks.