How are the net calories worked out?

you can go over in one and be under in another, depends on what you eat. If you eat a ton of lean protein you will go red and still have a lot of calories left.

I aim for red in protein, calcium, iron, and fiber, but stay under in calories, fat, and carbs.
It just means you are eating the right foods.
Unless it's RED in FAT and carbs but way under on protein and fiber, that would mean you are eating the WRONG foods.

Over on carbs is good only if you are also high in fiber, the bad carbs don't usually have the fiber, the good carbs do.

Basically, it's ok to be over in some categories, as long as you don't overdo the calories.

OK when you started with MFP you put in all your stats, in order to loose 1 pound you have to eat 3500 calories less a week in order to lose. MFP figures that into you daily allowance, but if you exercise it gives you some calories back . here is an example.
I need 2500 calories a day to live, I want to lose 2 pounds, thats - 1000 calories a day, so I get to have 1500 calories a day. OK now since I put my level as sedentary and I put in my garden and shovel dirt for 1 hour I put that in the exercise data base and it gives me a huge amount of calories back. Now in order to lose weight the right way I'm going to eat most of those calories back. You might ask why? ok for several reasons
1) I like eating and the idea that if I chose to I can have a higher calorie food when I work our for it( I dont feel deprived)
2) if you keep eating under you net calories for a while your metabolism slows down (yes you will still lose, but not as quick and you'll be gaining even quicker when you go back to maintenance)
3) this time I want to keep it off and it teaches me that if I want to eat pizza I have to work for it...
4) if you are constantly low on the net calories your body is more likely to also use your muscles as fuel and that is something I don't want.
On the going over part of fat or protein or carbs. I agree with most of the posts earlier. I don't mind if I go over on protein or healthy carbs, watch the sodium and fat. Sodium is not your friend, it keeps water in your system and you can "gain" 5 pounds after a restaurant meal, anf depending on what kind of fat it might not be the best idea either ( olive oil, fat from nuts, fish and some other sources are fine, fat from animals .... not so much)
My advise take it one day at a time, trust MFP on the calories and enjoy your jurney to being healthy and fit

Thanks for all the suggestions and comments. So, in a nutshell, if I keep within 50 calories of my daily calorie intake, without worrying too much about the other columns, then is that OK?

That's a good way to get started, but eventually you'll want to start researching and understanding macronutrient (fat, carb, protein) ratios and other nutrient amounts. Take it one step at a time first, though, and focus on calories for now.