select (select sum(col) as Total from Query1) - (select sum(col) as OtherTotal from Query2) as NewTotal

;WITH Query1 AS (
	SELECT 
		coalesce (cast(DATENAME(MM,hst_date_processed) as varchar(20)), 'Grand Total') as [Months],
		SUM(ffh.Net_Sales) AS [Sum Of Net Sales], 
		SUM(ffh.Net_Trans) AS [Sum Of Net Transactions]
	FROM Fact_Financial_History ffh 
	INNER JOIN Dim_Interchange_Tier_2 i 
		ON (ffh.hst_prod_code + '-' + ffh.hst_plan_code) = i.Plan_Code
	WHERE ffh.hst_date_processed >= @date
		AND ffh.hst_prod_code IN ('79','81')
		AND ffh.hst_plan_code IN ('002','010','011','015','037','033','021','019','020','030','029')
		AND I.Plan_Code <> '79-021'
	GROUP BY ffh.hst_date_processed 
		WITH ROLLUP
	--ORDER BY ffh.hst_date_processed desc
),

Query2 AS (
	SELECT * 
	FROM ( 
		SELECT 
			CASE 
				WHEN GROUPING(o.FDMSAccountNo_First9) = 1 THEN 'Grand Total'
				ELSE CAST(o.FDMSAccountNo_First9 AS VARCHAR(20))
				END AS FDMSAccountNo_First9,
			o.DBA_Name,
			SUM(ffh.Net_Sales) AS TotalofNetAmount, 
			SUM(ffh.Net_Trans)AS TotalofNetTransactions
		FROM Fact_Financial_History ffh 
		INNER JOIN Dim_Outlet o 
			ON ffh.hst_merchnum = o.FDMSAccountNo_First9
		INNER JOIN dbo.Dim_MCC 
			ON o.MCC_Code = dbo.Dim_MCC.MCC		
		WHERE ffh.hst_date_processed > @date 
			AND ffh.hst_prod_code BETWEEN '79' AND '84'
			AND o.MCC_Code = '5968' 		 
		GROUP BY 
			o.FDMSAccountNo_First9,
			o.DBA_Name
		WITH ROLLUP
	) AS temp 
	WHERE temp.DBA_NAME IS NOT NULL 
		OR temp.FDMSAccountNo_First9 = 'Grand Total'
)
SELECT WhateverYouWant
FROM Query1
INNER/LEFT OUTER/FULL OUTER JOIN Query2 
	ON Query2.somecolumns = Query1.somecolumns
ORDER BY SomethingMeaningful