I usually recommend that you eat enough to cover your BMR, then add a few more calories on top of this depending on how much exercise you do. So if you burn >500 in an exercise session, then just eat a bit more until your at an calorie deficit of about 500kcals or less or slightly more. If you only burn <500 or less then id just cover BMR and maybe a few hundred calories less.
You'll usually (if not always) dip into BMR when trying to drop scale weight, that's why its important to make weight loss a slow, steady process to avoid any damage or adverse results. If your only eating 1000 calories and your BMR is +/-2000 and your exercising on top of this great deficit (burning off say 500kcals) then your body can only use 500kcals for physiological functions. The rest may come from muscle, fat or by shutting down energy consuming functions which are non-essential in survival of the body (more understood in females, or just better documented).