Confused about calorie intake and exercise. Please help.

I always added the workout calories throughout the day. I usually workout at night so I will have my shakeology after because it's low calorie but high protein. I stay pretty close to my daily calorie allowance even after I workout.

Eat the 1290 PLUS the 250

You have misunderstood the selection of Activity level in your profile.

That is for your non-exercise part of the day ONLY.

Then your non-exercise eating goal is based on that, eating less than you burn with no exercise.

But when you exercise you burn more.
Take away the same deficit to lose the same amount of weight, and that means you eat more.

So to keep it simple - go back to your profile.
Select honest daily activity level that is NOT exercise included.
Sedentary is 45 hr desk job/commute, no kids, no walking to store or other, outside exercise just a bump on a log basically.
Select reasonable weight loss goal, 2 lb weekly is reasonable for you - for now.
At 50 lbs, switch to 1.5 lbs weekly.
At 25 lbs, switch to 1 lb weekly.
At 10 lbs left, switch to 0.5 lb.

Set your exercise goals at whatever you want - they have NO bearing on your eating levels, they are goal that are ONLY seen on your Fitness diary. If you haven't noticed them yet, or they don't encourage to workout more or whatever, ignore them and set to whatever. Again, no math from them is applied to Diet goals.

When you do 250 cal of exercise, you log it. Your daily burn just went up by 250 calories.
So now your eating level goes up 250 calories also.

But either way - you have 1000 cal deficit to your estimated daily burn.

The idea being you do NOT want an unreasonable deficit. Because losing more faster is not always better, unless you want to lose muscle mass too. You'll want that later.

So you saw your goal was 1560, and you were willing to eat that without knowing where that number came from or why or what it was.
Now the number is 1290.
When you log the exercise of 250 cal burn the number will be 1540.
Just keep eating to the goal that is stated on your Food diary and you'll be alright.
And 50 over is better than 100 below on constant basis. If you are willing to miss 100, then be willing to eat 100 more the next day.
Would you miss your goal weight by 20% and say close enough?

Basically MFP tries to keep it simple by having a NET goal that is the same with or without exercise, though the fact is you eat more on days you exercise because you indeed burn more.

I liked the way that you broke everything down. I went back to my profile as you stated and followed everything thoroughly. I changed my activity level back to lightly active like I originally had it as, and my weight loss goal is set at 2 lb weekly.. My net calories consumed/day is 1,560 calories a day. My fitness goals say 2,450 calories a week. My daily calorie deficit is 1,000 calories. So this calorie deficit was derived from the 2,560 calories from normal daily activity minus my daily calorie goal. This means that as long as I eat the 1,560 calories regardless of working out that I should still lose 2 pounds a week.

Mostly correct.

Not regardless of working out though, that's the daily goal on non-exercise days. Just to make sure I read that right.

So notice the 2560 is estimated calorie burn from daily activity - no exercise included.

But you do a workout of 300 calories...
2560 + 300 = 2860 daily burn with exercise.

2860 - 1000 deficit = 1860 eating goal for this day.

In reality though, MFP keeps it simple (supposedly) by just adding the 300 to your eating goal. But now you see what is happening in reality. You lose weight by eating less than you burn, and MFP makes it the same amount less no matter what you burn.

If you do some sort of exercise every day, even if that is walking the dog for 45 min on a "rest" day, you'll never be eating 1560, but always some amount more.
Your NET though will always be 1560. But what you'll actually eat is more.

Just don't make the mistake of logging as exercise parts of your daily life already included in Lightly Active. Like house/laundry cleaning almost daily because you have kids, or your job is half standing time, or walking between classes, ect. Those are already included in Lightly Active.
Only the extra stuff, like walking the dog when someone else doesn't, or doing extra 30 min of walking laps around campus, ect, would you log as workout and basically eat it back.

Just be honest with logging too. Don't estimate walking/jogging speeds. If you have regular route, use a mapping site to get the distance, and then time yourself to get avg speed. If on treadmill, the fact you worked your way up to 4 mph eventually doesn't mean the whole 60 min was at 4 mph, take total distance and time done for true average.

1860 calories is a lot to eat.. I am already trying to space food out throughout the day just to reach close to 1,560.. It makes me feel like I shouldn't work out if I'm going to have to eat more. My net calories are never 1,560. They always end up being less than 1,000 most of the time, and always trying to figure out what I can eat to increase them. So this means that if I don't work out on a certain day then I should be consuming the full 1,560 calories, not more than that.

Then you have no idea how much you use to eat to gain weight, and you are being too restrictive with your diet now.

Because you ate more than 2500.

Now, you don't have to eat the same bad foods, but you may be defining healthy foods you are willing to eat too restrictive.

For instance, you need fat, fat is major regulator of hormones and healthy body, just eat healthy fats.

So think about this, if you are already eating that low, you should be losing 3 lbs weekly or over. But I'll bet you aren't.

And as you weigh less down the road, you will burn less just moving around, and of course to keep losing, you'll have to eat less then.

If you are eating that low already - where exactly do you think you'll go to eat less? Or are you going to massively exercise to make up the difference?
And with that method, if you get sick or injured or take a vacation and can't workout that much - what then, now you'll have to eat a ton less to keep losing same amount?

And the type of exercise is indeed a good point. You'd be better served doing some resistance training - because at this point you don't need more calories to eat to adhere to a diet, which is what burning more gets you.
So do some circuit training. When you log that, it's a smaller calorie burn than lots of cardio, plus it'll help retain muscle mass.
Which will set you up better down the road.

And just be aware, when you eat too little, you do screw up hormones that would cause normal hunger signs.
You feeling full, and your body being fully fed for your level of activity - are 2 very different things and not related.
Trust your brain, not your stomach, doing that backwards gets many to this point.
You can't trust your body, because the time to find out is too long and damage is done. Much like vitamin or mineral deficiency - the symptoms show up much farther down the road, and in some cases very serious side effects and it takes awhile to get body balanced back out.