Sorry for the stupid question but...

MFP calorie goals allow for you to eat back some or all of the calories you burned off while working out, as long as your net calorie intake for the day is below your goal. So a daily goal of 1500 calories + 500 calories burned with exercise allows you to eat 2000 calories a day and still hit your net calories for the day. Hope that helps.

Net = Food - Exercise. Remaining = (Goal + Exercise) - Food. Ideally you want to get Remaining reasonably close to 0, by eating Goal + Exercise.

Some people eat back exercise calories and some do not. Really it's up to you, but the reason your calorie remaining changes is because the goal is to maintain a consistent calorie deficit for controlled weight loss. For instance MFP has calculated my Calories Burned from normal daily activity as 2840 cal/ day (based on my specific measurements and a lightly active lifestyle). To loose 2 lbs per week it subtracts 1000 calories to give me a daily calorie goal of 1840. But if I go for a run and burn 260 calories beyond my normal daily activity MFP adds that to my total meaning that I burned 3100 cal (2840 from normal activity + 260 from the run). To maintain the constant 1000 calorie deficit I should eat 260 extra calories.

Normal Day
2840 cal burned with no additional exercise
1840 cal consumption allowed

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-1000 cal = 2 lbs/ week lost

With exercise
2840 burned with no additional exercise
+260 for the run

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3100 calories burned
-1000 to maintain 2 lb/ week loss

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2100 cal consumption allowed because of exercise

After I add an exercise, my calorie goal raises. Which calorie goal do I use? Do I stay within my "Net" calorie goal or the amount that says "Remaining" Thanks I know this is probably something I shoud know but want to make sure I am doing this right.

Your remaining should be as close to zero as possible, providing your exercise calories are accurate.

This will help - http://www.myfitnesspal.com/topics/show/818082-exercise-calories-again-wtf