I suspect part of the answer is familiarity with the food. What is it supposed to look like? What is it supposed to smell like? How do things change after a certain amount of time? What should the texture be? What should it feel like either to the hand or through a utensil? How would you know if it's too much of something, and how do you fix it?
For example, when thinking of a risotto, the basic technique is to saute the rice with some oil and other flavorings (such as onion), then put in hot broth a little at at time, stirring until it is absorbed, and then repeat until the rice is the right texture. Then once it is, finish the dish by adding the last flavorings. (Things such as cheese, which would be damaged by too much heat.)
For meats, so long as you know the temperature you're trying to reach (and have a good thermometer), the rest is playing around with flavorings and making sure it looks/smells as good as possible. (Which would mean things like starting with a high-temperature sear to get some nice browning before lowering the tempurature enough to cook it all the way through.)
Ratios are important in baking, but in most cooking, I suspect it's more about understanding how the ingredients interact. For example, take something basic like onions. What happens when it's raw? How about only slightly cooked? High temperature versus low? Wet cooking versus dry cooking? Each of these things would affect how the final dish would come out, and you plan when to add the onion based on which of these flavors you want to achieve.
I have the best results when I cook a recipe over and over, and start playing with some of the variables. For example, when I make a stir fry, I vary which vegetables I put in when, and how they're cut will affect that. I play with the seasonings and try different combinations added at different times. The more I do it, the better feel I have for what's possible and what's tasty. I think that's why the best cooks can go without recipes -- they're working from so much experience that they can do it without questioning how they understand it.