Creating dishes, am I doing it right?

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So when i first came to MFP I mostly added menu items from the huge database it has however more and more I'm now finding that the items I want to add, because they are custom home made by me aren't in there or aren't accurate for ingredients. As such I have started to add my own to my personal food database.

The question really is how do you create your recipes/dishes/foods?

Generally I will add all ingredients to the list as raw ones, for example if i make a pie, I will add to the ingredients the pastry in its un cooked, weight/form. Then the meat in the same manner and veg/anything else going in etc etc. If its something fried I will add the oil used in cooking etc. Then i just cook the dish and eat it, but the calories from the disk I created are purely based on their raw values/weight.

My concern is that a quick look around the internet has revealed that in some cases food after being cooked and both gain and loose calories, losing them makes sense, if you grill something and some of the calories come out during the process, but i'm not sure how something can increase in calories, unless of course you are adding them by other means (like glaze, or oil etc). So i figure the worse that can usually happen is I over estimate and when i say my meal is 500 calories, due to cooking it may actually be 450, but what I wonder is what are the chances that if no extra factors are ADDED, that it could in fact be over 500 and causing my diet harm.

Thanks for reading and any insights you lovely people might have.