Help, I'm confused! New to MFP

I can only help with a couple... If your number turns red you ate more then you have burned. With sodium if you get to much it is unhealthy. So dont think of it as dieting, cause then when you are done you will go back to doing what got you here. Think of it as a life style change. Start educating yourself on foods and what each thing does for your body, and what they do if you have to much. Sodium has a lot of bad if you go over but the first thing that comes to mind is that it will make it much harder for you to see the weigh come off. It sends your body into water retention. I hope this helps. I look forward to seeing others answer the rest of your questions,

Are net calories "extra calories" that I can eat during the day?

MFP sets a calorie goal for you without taking exercise into account. When you log your exercise it adds the extra calories you earn to your goal. You should eat at least a portion of these to help fuel your body and retain your lean muscle mass. MFP sets up a reasonable goal for you with a calorie deficit built in. When you exercise you make this deficit larger, possibly larger than your body can safely handle. Eating back some of those exercise calories helps to bring you back into that original, safe calorie deficit.

That said, be aware that MFP and gym machines have a tendency to overestimate your calories burned. Eating back 50-75% of your exercise calories is usually a good idea to make sure you're not eating too much.

What happens when the number turns RED?

Nothing. If you're still under your TDEE for the day (Total Daily Energy Expenditure - the number of calories you could eat to maintain your current weight) you will still lose weight, though possibly a little slower. If you go over that number, you may or may not lose weight depending on how often and by how much.

If I go over sodium or sugar, can I still lose weight if I am still under 1440 calories a day?

Sodium and sugar will not affect your weight loss. If you have no medical conditions to worry about, I'd even recommend replacing those trackers with something like Fiber & Calcium/Iron/Potassium, etc. For weight loss, calories are the only thing that matter. Eating more proteins and fats will keep you fuller and help you retain more of your lean muscle mass, but start with the calories.

Which brings us to another point, the protein default is set pretty low here. If you're using MFP's default numbers think of protein as a minimum goal not a maximum.

Whats the difference between calories REMAINING verses NET CALORIES?

Remaining calories are the number of calories you can still eat and be within the goal that MFP sets for you. NET calories are the number of calories you've eaten today minus the number of calories you've burned through exercise.

Should I always eat my NET?

You should eat until your NET reached your original MFP goal (1440) within reason, see point 1.