The food goes in and gets broken down to differing sizes based on various enzymes in your gut, passed into your system and distributed according to built in pathways. The issue you're having is with falling for the basic assumption that most people have when it comes to nutrition. When you eat a turkey leg you don't grow an additional leg; when you eat chicken livers it doesn't only go to nourishing your liver, and when you drink a Pepsi you don't start sprouting an aluminum can somewhere in your body. The same goes for things like fats, proteins and carbs (to an extent). Fats and proteins are indeed used as building blocks in your system but many of them are so torn apart by the digestive enzymes mentioned above that they can be sent to many different places to build many different structures. When you consume too much of this some may be stored for later but the vast majority of it that is not used gets deposited next time you visit the commode.
Carbohydrates unfortunately only really have one purpose and that's to provide quick energy. It's also severely toxic and life threatening in large enough concentrations in your blood. Because of it's potential life ending effects the body has to work to get the stuff out of commission (see insulin) Additionally your body is pretty darned good at storing carbs for later usage. Some is stored as glycogen however the primary storage location for excessive carbohydrates is fat cells. Fat cells are our bodies storage sites, they're not just places where last night's steak trimmings ended up clumping together.
Things really start getting shifty once insulin resistance enters the picture which you run the risk of if you're in a chronically insulin heavy state.