MySQL Calculate percentage difference (not change) between 2 columns
With some help the solution was to use a subquery something like this: 

SELECT
  CONCAT('£ ', t1.n1) AS N1,
  CONCAT('£ ', t1.n2) AS N2,
  CONCAT(((N1 - N2) / ((N1 + N2) / 2)) * 100, ' %') AS 'Difference' 
FROM (SELECT
    SUM(CASE WHEN t1.col_type = 'N1' THEN t2.qty * t1.price ELSE 0 END) AS n1,
    SUM(CASE WHEN t1.col_type = 'N2' THEN t2.qty * t1.price ELSE 0 END) AS n2
  FROM t2
    INNER JOIN t1
      ON t2.col_id = t1.col_id) t2