How many calories your burning, do you count your net calories as your total for the day, or do you count everything even though you burned x amount?

You minus what you burned and that's your total.

I keep calories in and calories out separate. I plan to eat between 600-700 calories a day (and manage my diet according to that number), and burn between 1,000 and 1,200 calories every time I go to the gym (4-5 days a week). My intake doesn't change much on the days I don't go to the gym (typically over the weekend). Even tracking on Myfitnesspal, I pay little attention to the "net calories," or the calories that system "thinks" I have left to eat for the day.

I guess it really depends on what kind of data tracking you are wanting to do. My doc told me to eat X amount of calories, and workout a certain amount. The X calories for me isn't necessarily a sliding scale, but it is worth considering especially if your workouts vary, or you only workout certain days of the week. By that I mean, don't necessarily eat less on days you don't workout, but you might consider eating more on heavy workout days otherwise you could be inhibiting your weight loss by having too big of a negative calorie deficit.

I never netted out the calories - the exercise "calories" recorded by the gym machines or listed in various tables aren't all that accurate so it never made sense to me to try to compare one against the other; I generally cut the numbers in half when I did my mental calculations of what I was doing, and then just did a weekly tally to track exercise progress apart from dietary progress. I let my body tell me if I needed to make adjustments to the diet. That way I didn't fall into the trap of "gee, I worked off an extra 500 calories today, so I deserve a....."