MFP Net calories v. Food (Help please!!)

 I use MFP to track everything I eat and any exercise I may do (I walk about 2.5 miles a day). I was wondering if I should go by my Net Calories or just my total calories for a day, which I am keeping around 650, my sugar around 15, and my carbs no more than 40. My doctor has not told me to increase or decrease my calories, but my NUT said not to count calories, just eat healthy foods and get enough protein (I'm getting about 70g/day). I've read so much about counting calories and carbs. I am almost 7 weeks post-op. Any suggestions?! 

Since surgery I have lost 32.4lbs, but had a 3 week stall from week 3- week 6. 

I use calories consumed, not NET.  Net is what you are eating OVER exercise or UNDER exercise.  

I never bothered with Net anything.. cals/carbs.. I did not try eating back any calories from activity (what Net is doing) as I figured I had plenty of fat reserves to tap into for energy!

I just stayed in the range of 600-800 till goal, ate around 20g total carbs with very little to no sugar (I don't track sugar as I avoid it completely for the most part, plus your body does not differentiate sugar from sucrose vs from starches like grains/potatoes.. all get converted to glucose very quickly during digestion and have the same effect on insulin) and 70+ protein. Not saying this is the plan you should follow, or anyone- just what I know my body does best at.

I am still low-carb but not that low as I eat far more veggies now and fiber, but still stay under 50g total, and prob will be low-carb for life as when those go up, my overall energy heads down and I gain/get nibbly.

For the first 15 months, I didn't net.  As I got closer to goal and I didn't have as much in the way of fat reserves, I started to net, or eat back some of my exercise calories.  As you get closer to goal, it becomes counterproductive to create too much of a calorie deficit.  You need to fuel your body to burn the last of the fat.  But you really don't have to worry about that until you're nearing the end of weight loss.