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Calories vs. Net Calories

To lose about 2lbs a week I'm eating 1500 calories a day. However when I add in my exercise the calories I've consumed seem to get subtracted and I am in the 900 calorie range. I'm not hungry throughout the day and I struggle to get to 1500 calories. My goal is to reduce body fat as I lose weight. Having 25% body fat is more important to me than reaching a set number on the scale.

I'm concerned that I might lose muscle mass if not eating the right caloric amount for my RMR. I thought this tracking app would help but I'm more confused then ever. Do I focus on total calories consumed or net calories? I had a Dexa scan and RMR test so I know what my numbers are. I just need to make sure I'm not losing muscle and eating enough.