How would I go about storing spawned prefabs to acces them ?

I have searched already and found out that I need a twodimesnional array, and its easier thatn it probably sounds but I quite still don’t get it.
So how does one put GameObjects in a twodimensional array or arraylist?

Are you talking about storing an instantiated prefab to access later? You don’t need a 2D array for that. Just do something like this-

GameObject  obj = Instantiate(prefab , position, quaternion.identity);
//you've just instantiated a prefab, and 'obj' now holds your instantiated prefab.

For a situation like this, a generic collection like List <> is probably your best bet.

If for example you want to add all spawned enemies to a single list to manage them you could do this:

public Enemy enemyPrefab;
private List <Enemy> spawnedEnemies = new List<Enemy>();

private void SpawnEnemy (Transform location)
     Enemy newEnemy = (Enemy)Instantiate (enemyPrefab, location.position, location.rotation);
     spawnedEnemies.Add (newEnemy);

The Instantiate function returns a reference to the spawned object. You can put that into an array:

var width = 10;
var height = 10;
var arr = new GameObject[width, height]; // for example

for(var x = 0; x < width; x++)
  for(var y = 0; y < height; y++)
    arr[x, y] = Instantiate(prefab, new Vector3(x, 0, y), Quaternion.identity);