Выберите его, затем сгруппируйте;
SELECT SUM(EntryValue) AS EntryValueTotal, EntryType, Left(Warehouse,1) AS Branch
...
GROUP BY Left(InvJournalCtl.Warehouse,1), EntryType
Редактировать Я не понял, что вы хотите вычесть;
SELECT
SUM(CASE EntryType
WHEN 'C' THEN EntryValue
ELSE 0 END
)
-
SUM(CASE EntryType
WHEN 'D' THEN EntryValue
ELSE 0 END
) AS EntryValueTotal,
Left(Warehouse,1) AS Branch
FROM GenJournalDetail
INNER JOIN InvJournalCtl ON (GenJournalDetail.GlPeriod = InvJournalCtl.LedgPeriod) AND (GenJournalDetail.GlYear = InvJournalCtl.YearPostLedg) AND (GenJournalDetail.Journal = InvJournalCtl.GlJournal)
WHERE
GenJournalDetail.GlCode = 'Z5207550' AND GlYear = '2011' AND GlPeriod = '10'
GROUP BY Left(InvJournalCtl.Warehouse,1)