I am not an expert, however I have lost 74 lbs in the last year and learned alot. I too was always seeing net negative numbers in the beggining. I ended up burning out eventually, my weight loss would stall, energy went down, I couldnt push myself as hard and I even got sick feeling during/after workouts alot.
So now what I have realized it that for me at least I try to never NET under my BMR....and if I do my wieght loss will stall or even go up and I still have 50-70 pounds left to lose. So my NET is about 1600, so I always eat at least 1600...but then if i go for a run or do a workout that is not factored into those calories and burn another say 200, then I would eat those back so that my NET would still be 1600.
Me personally have my calories set to 2000, becuase most days I burn at least 400 in exercise. I just find it easier to plan my day with those extra calories instead of trying to fit them in later...and if I burn over 500 calories I try to eat back that too, or else my NET would be below 600.
I use this site it is great, and I know LOTS of people who have had success following the reccomended calories it gives. http://www.fat2fitradio.com/tools/bmr/
However everybody is different so you will need to learn your body and what works for you...also just so you know if you start eating more, you will most likely gain weight until your body adjusts, then your matabolism speeds up and you will be losing again.
hope this was helpful!