Melt the margarine in a small pot. Add the flour to create a roux. I usually cook it only a minute or two but if you want a deeper toastier flavour you can keep cooking it till it's dark enough for you. Anyway, whisk your roux constantly. If it burns, throw it out and start over.
Once it's cooked to your satisfaction, add the water and whisk thoroughly. Leave no bumps! Whisk in the nutritional yeast and the seasonings, to taste. I use a generous dash of soy sauce, a little smidgen of mustard, several good shakes of the garlic salt jar, a few cranks of the pepper mill, and about 3 shakes of the cayenne jar.
Simmer till it's thick enough for you. You can use this on nachos, pizza, macaroni, whatever. Enjoy! Nutritional yeast is an excellent source of vitamins, especially B-complex, minerals, and amino acids.