Yes, you are right:
WHEN merch_purch_fees < 0 THEN [Merch_Purch_Fees]
WHEN merch_purch_fees > = 0 THEN [Merch_Purch_Fees] + [Per_Tran_Fees]
) AS MSCTEST
WHERE FDMSAccountNo = '878031202889'
Also, if there is a possibility that [Per_Tran_Fees] would be null (or merch_purch_fees would be null), you should account for that, for example like this:
WHEN COALESCE(merch_purch_fees,0) > = 0 THEN COALESCE([Merch_Purch_Fees],0) + COALESCE([Per_Tran_Fees],0)