Which column did you want to make negative? Just multiple by -1.
For example, "[FY16]-[FY15] AS [YoY Var]".
To make it negative : ([FY16]-[FY15]) * -1 AS [YoY Var]
You really need work on your naming convention.
Suggestions:
Don't use spaces in object names.
Don't use punctuation in object names.
Don't use special characters in object names.
You have "[YoY Var (%)]" and "ctAccountGrouping-PYvsCY" (a dash)
And your table/query names!!... They are sooooo long, you should think about using aliasing.
Code:
SELECT TTG.[Trend Type], AGPYCY.[Grouping Category], AGPYCY.FY15, AGPYCY.FY16, [FY16]-[FY15] AS [YoY Var], [YoY Var]/[FY15] AS [YoY Var (%)]
FROM ([Trend Type Grouping] TTG INNER JOIN [Account Grouping] AG ON TTG.[Account Number] = AG.[Account Number]) INNER JOIN [ctAccountGrouping-PYvsCY] AGPYCY ON AG.[Grouping Category] = AGPYCY.[Grouping Category]
GROUP BY TTG.[Trend Type], AGPYCY.[Grouping Category], AGPYCY.FY15, AGPYCY.FY16
ORDER BY TTG.[Trend Type];