--one way is to use union all to get all rows then you perform the GROUPING once on the entire set.
SELECT dbo.tblBasicPermitFeeSchedule.RecId, dbo.tblBasicPermitFeeSchedule.CertType,
COUNT(dbo.tblRequests.RequestNo) AS Quantity
FROM dbo.tblCedula INNER JOIN
dbo.tblRequests ON dbo.tblCedula.RequestNo = dbo.tblRequests.RequestNo
RIGHT OUTER JOIN
dbo.tblBasicPermitFeeSchedule ON dbo.tblRequests.CertType = dbo.tblBasicPermitFeeSchedule.RecId
UNION ALL
SELECT dbo.tblBasicPermitFeeSchedule.RecId, dbo.tblBasicPermitFeeSchedule.CertType,
COUNT(dbo.tblRequests.RequestNo) AS Quantity
FROM dbo.tblBarangayClearance INNER JOIN
dbo.tblRequests ON dbo.tblBarangayClearance.RequestNo = dbo.tblRequests.RequestNo
RIGHT OUTER JOIN
dbo.tblBasicPermitFeeSchedule ON dbo.tblRequests.CertType = dbo.tblBasicPermitFeeSchedule.RecId
GROUP BY dbo.tblBasicPermitFeeSchedule.RecId, dbo.tblBasicPermitFeeSchedule.CertType
--another way is to use a subquery
SELECT dbo.tblBasicPermitFeeSchedule.RecId, dbo.tblBasicPermitFeeSchedule.CertType,
COUNT(dbo.tblRequests.RequestNo) AS QuantityRequests.
(
SELECT dbo.tblBasicPermitFeeSchedule.RecId, dbo.tblBasicPermitFeeSchedule.CertType,
COUNT(dbo.tblRequests.RequestNo) AS Quantity
FROM dbo.tblBarangayClearance
INNER JOIN dbo.tblRequests
ON dbo.tblBarangayClearance.RequestNo = dbo.tblRequests.RequestNo
RIGHT OUTER JOIN dbo.tblBasicPermitFeeSchedule
ON dbo.tblRequests.CertType = dbo.tblBasicPermitFeeSchedule.RecId
GROUP BY dbo.tblBasicPermitFeeSchedule.RecId, dbo.tblBasicPermitFeeSchedule.CertType
) AS QuantityRequestNo
FROM dbo.tblCedula
INNER JOIN dbo.tblRequests
ON dbo.tblCedula.RequestNo = dbo.tblRequests.RequestNo
RIGHT OUTER JOIN dbo.tblBasicPermitFeeSchedule
ON dbo.tblRequests.CertType = dbo.tblBasicPermitFeeSchedule.RecId