You have some errors on the way you want to generate the query. You can't combine the assignment of variables with the return of results and you need to write a CASE for each column on your query (at least).
However, I don't understand why would you want to count a value returned by a formula. Wouldn't you need to use SUM?
Here's my interpretation from your query. I have nothing to test and I don't know what you expect from this. For better answers, please read the article linked in my signature.
ALTER PROCEDURE DoubleSidedSheets @StartDate DATETIME,
@EndDate DATETIME,
@SCount INT = 0,
@DCount INT = 0,
@DSheets INT = 0,
@SSheets INT = 0
AS
SELECT Right(rpt.[Cost Center], 4) AS [Cost Center Name],
rpt.[User Id] AS [User ID],
CASE
WHEN rpt.Pages = rpt.[Sheets]
THEN @SCount + rpt.[Sheets]
ELSE @SCount + (Sheets - (Pages / 2))
END AS [Single Sided Print],
CASE
WHEN rpt.Pages = rpt.[Sheets]
THEN @DCount = 0
ELSE (Pages / 2) + @DCount
END AS [Double Sided Print]
FROM rpt_print_transactions rpt
WHERE rpt.[Date/Time] >= @StartDate
AND rpt.[Date/Time] <= @EndDate
GROUP BY rpt.[Cost Center],
rpt.[User Id]
GO
---OR
ALTER PROCEDURE DoubleSidedSheets @StartDate DATETIME,
@EndDate DATETIME,
@SCount INT = 0,
@DCount INT = 0,
@DSheets INT = 0,
@SSheets INT = 0
AS
SELECT Right(rpt.[Cost Center], 4) AS [Cost Center Name],
rpt.[User Id] AS [User ID],
SUM(CASE
WHEN rpt.Pages = rpt.[Sheets]
THEN @SCount + rpt.[Sheets]
ELSE @SCount + (Sheets - (Pages / 2))
END) AS [Single Sided Print],
SUM(CASE
WHEN rpt.Pages = rpt.[Sheets]
THEN @DCount = 0
ELSE (Pages / 2) + @DCount
END) AS [Double Sided Print]
FROM rpt_print_transactions rpt
WHERE rpt.[Date/Time] >= @StartDate
AND rpt.[Date/Time] <= @EndDate
GROUP BY rpt.[Cost Center],
rpt.[User Id]
GO