CREATE TABLE #tmp
	(Key1 VARCHAR(10),
	Key2 VARCHAR(10)
	)

CREATE TABLE #tmp2
	(Key1 VARCHAR(10),
	Key2 VARCHAR(10),
	Key3 VARCHAR(10),
	Key4 VARCHAR(10)
	)

INSERT INTO #tmp VALUES	('aa', 'bb')
INSERT INTO #tmp VALUES ('cc', 'dd')
INSERT INTO #tmp VALUES ('ee', 'ff')
INSERT INTO #tmp VALUES ('gg', 'hh')

INSERT INTO #tmp2 VALUES ( 'aa', 'zz', 'abc', 'def')
INSERT INTO #tmp2 VALUES ( 'bb', 'ee', 'abc', 'def')
INSERT INTO #tmp2 VALUES ( 'cc', 'gg', 'abc', 'def')
INSERT INTO #tmp2 VALUES ( 'dd', 'zz', 'abc', 'def')

SELECT	Key1, Key2
from	#tmp
EXCEPT
SELECT Key1 FROM #tmp2

Msg 205, Level 16, State 1, Line 2
All queries combined using a UNION, INTERSECT or EXCEPT operator must have an equal number of expressions in their target lists.

INSERT INTO PortSecAgg
	(PortfolioID,
	SecurityID,
	AsOfDate,
	IsShortPosition,
	PortfolioCode,
	Symbol,
	Quantity,
	SectypeCode,
	Cusip,
	UnitCost,
	TotalCost,
	Price,
	MarketValue,
	AccruedInterest,
	UnrealizedGL,
	IsSubAccount
	)
SELECT
	vpsa_s.PortfolioID,
	vpsa_s.SecurityID,
	vpsa_s.AsOfDate,
	CASE WHEN vpsa_s.Quantity < 0. THEN 1 ELSE 0 END AS IsShortPosition,
	vpsa_s.PortfolioCode,
	vpsa_s.Symbol,
	vpsa_s.Quantity ,
	vpsa_s.SectypeCode,
	vpsa_s.Cusip,
	vpsa_s.UnitCost,
	vpsa_s.TotalCost,
	vpsa_s.Price,
	vpsa_s.MarketValue,
	vpsa_s.AccruedInterest,
	vpsa_s.UnrealizedGL ,
	CASE WHEN vpsa_s.IsSubAccount = 'Y' THEN 1 else 0 END AS IsSubAccount
FROM 
	vw_PortSecAgg_Staging AS vpsa_s
	LEFT JOIN
		PortSecAgg AS psa
	ON	psa.PortfolioID = vpsa_s.PortfolioID
		AND psa.SecurityID = vpsa_s.SecurityID
		AND psa.AsOfDate = vpsa_s.AsOfDate
		AND psa.IsShortPosition = vpsa_s.IsShortPosition
WHERE
	psa.PortfolioID IS NULL

SELECT key1, key2 FROM #tmp
EXCEPT
SELECT key1, key2 FROM #tmp2

;WITH updates ({list of columns for the CTE here})
AS (
SELECT key1, key2 FROM #tmp
EXCEPT
SELECT key1, key2 FROM #tmp2
     )
SELECT *
   INTO #updates
   FROM updates;

UPDATE alias
     SET ...
   FROM YourFinalTable t
  INNER JOIN #updates u ON u.key1 = t.key1 ...

INSERT INTO YourFinalTable (...)
SELECT ...
   FROM YourFinalTable t
   LEFT JOIN #updates u ON u.key1 = t.key1 ...
  WHERE u.key1 IS NULL;

select #tmp.key1, #tmp.key2 FROM #tmp
inner join 
	(
		SELECT key1 FROM #tmp
		EXCEPT
		SELECT key1 FROM #tmp2
	) q on #tmp.key1 = q.key1