WHEN BODY IS THROWN UPWARDS THEN ACCELERATION DUE TO GRAVITY IS NEGATIVE OR POSITIVE?

Please read the following paragraph carefully and you will have no problems in the same topic again:

For the study of physics, we use equations. But equations work with numbers, right? Yes!

So, to use values from real life in equations, we have to find a way to accurately represent the situation into numbers.

But, what happens when we are dealing with a change in direction, in maths? Suppose you are moving in a car in a straight line with a velocity V. Then you take a U-turn and keep on moving with the same velocity. But, you cannot tell an equation to turn around at the next U-turn , can you? 

To deal with this, what we do is consider the car to be moving backwards or negatively. So, when the car is moving forwards, we consider the velocity to be positive, and when backward, it is considered to be negative.

But forwards and backwards from where? You need a point from where you will need to move forwards or backwards, right?

We shall try to understand this with an example:

Consider the ball kept on the ground. 

First, we consider it's initial position and we mark it as origin. Now, when it moves right from it's initial position, we call it's displacement positive, and when it moves left we'll call it negative. (We could use right as negative as well, it totally depends on us)

Similarly for the directions up and down.

Now, with this sign convention in your mind, consider the acceleration due to gravity. It will always be towards the ground. An object thrown upwards will always fall back, no matter what the direction of the motion. So if you take the downward direction as positive, the acceleration due to gravity is negative, if you take down as positive, it will be positive.

Negative and positive are only the signs used to denote the direction in the sign convention WE CHOOSE.

Please do not hesitate to ask again if you still have a doubt!