It is not so simple. If you eat 3000 calories of just carbs, any excess will be stored as fat. If you eat 3000 calories of just fat, your body will flush most (all?) of the fat it does not use for energy. Part of the reason Atkins works so well is because it forces your body to go into ketosis. Ketosis makes it so your body burns fat for energy instead of carbs.
I am not expert on the subject by any means but I have gathered this much from my own research. Whoever told you that all calories are equal do not know what they are talking about.