How to improve query to include 2 critical pieces of employee data
Without the schema this is a little difficult to test but I think this will work. Even if I do make some syntax errors you will be able to see what I am getting at.

SELECT
    PayrollpersonID, 
    PayrollDeductionYear, 
    SUM(CASE WHEN PayrollDeductionMonth = 'January' THEN Variance ELSE 0 END) AS January, 
    MAX(CASE WHEN (PayrollDeductionMonth = 'January' AND PayrollDeductionAmount = 0 AND invoice &gt; 0) THEN 1 ELSE 0 END) AS 'January No Deduction',
    MAX(CASE WHEN (PayrollDeductionMonth = 'January' AND PayrollDeductionAmount &gt; 0 AND invoice = 0) THEN 1 ELSE 0 END) AS 'January No Invoice',
    SUM(CASE WHEN PayrollDeductionMonth = 'February' THEN Variance ELSE 0 END) AS February, 
    MAX(CASE WHEN (PayrollDeductionMonth = 'February' AND PayrollDeductionAmount = 0 AND invoice &gt; 0) THEN 1 ELSE 0 END) AS 'February No Deduction',
    MAX(CASE WHEN (PayrollDeductionMonth = 'February' AND PayrollDeductionAmount &gt; 0 AND invoice = 0) THEN 1 ELSE 0 END) AS 'February No Invoice',
    SUM(CASE WHEN PayrollDeductionMonth = 'March' THEN Variance ELSE 0 END) AS March,
    MAX(CASE WHEN (PayrollDeductionMonth = 'March' AND PayrollDeductionAmount = 0 AND invoice &gt; 0) THEN 1 ELSE 0 END) AS 'March No Deduction',
    MAX(CASE WHEN (PayrollDeductionMonth = 'March' AND PayrollDeductionAmount &gt; 0 AND invoice = 0) THEN 1 ELSE 0 END) AS 'March No Invoice',
    SUM(CASE WHEN PayrollDeductionMonth = 'April' THEN Variance ELSE 0 END) AS April,
    MAX(CASE WHEN (PayrollDeductionMonth = 'April' AND PayrollDeductionAmount = 0 AND invoice &gt; 0) THEN 1 ELSE 0 END) AS 'April No Deduction',
    MAX(CASE WHEN (PayrollDeductionMonth = 'April' AND PayrollDeductionAmount &gt; 0 AND invoice = 0) THEN 1 ELSE 0 END) AS 'April No Invoice',
    SUM(CASE WHEN PayrollDeductionMonth = 'May' THEN Variance ELSE 0 END) AS May, 
    MAX(CASE WHEN (PayrollDeductionMonth = 'May' AND PayrollDeductionAmount = 0 AND invoice &gt; 0) THEN 1 ELSE 0 END) AS 'May No Deduction',
    MAX(CASE WHEN (PayrollDeductionMonth = 'May' AND PayrollDeductionAmount &gt; 0 AND invoice = 0) THEN 1 ELSE 0 END) AS 'May No Invoice',
    SUM(CASE WHEN PayrollDeductionMonth = 'June' THEN Variance ELSE 0 END) AS June, 
    MAX(CASE WHEN (PayrollDeductionMonth = 'June' AND PayrollDeductionAmount = 0 AND invoice &gt; 0) THEN 1 ELSE 0 END) AS 'June No Deduction',
    MAX(CASE WHEN (PayrollDeductionMonth = 'June' AND PayrollDeductionAmount &gt; 0 AND invoice = 0) THEN 1 ELSE 0 END) AS 'June No Invoice',
    SUM(CASE WHEN PayrollDeductionMonth = 'July' THEN Variance ELSE 0 END) AS July, 
    MAX(CASE WHEN (PayrollDeductionMonth = 'July' AND PayrollDeductionAmount = 0 AND invoice &gt; 0) THEN 1 ELSE 0 END) AS 'July No Deduction',
    MAX(CASE WHEN (PayrollDeductionMonth = 'July' AND PayrollDeductionAmount &gt; 0 AND invoice = 0) THEN 1 ELSE 0 END) AS 'July No Invoice',
    SUM(CASE WHEN PayrollDeductionMonth = 'August' THEN Variance ELSE 0 END) AS August, 
    MAX(CASE WHEN (PayrollDeductionMonth = 'August' AND PayrollDeductionAmount = 0 AND invoice &gt; 0) THEN 1 ELSE 0 END) AS 'August No Deduction',
    MAX(CASE WHEN (PayrollDeductionMonth = 'August' AND PayrollDeductionAmount &gt; 0 AND invoice = 0) THEN 1 ELSE 0 END) AS 'August No Invoice',
    SUM(CASE WHEN PayrollDeductionMonth = 'September' THEN Variance ELSE 0 END) AS September, 
    MAX(CASE WHEN (PayrollDeductionMonth = 'September' AND PayrollDeductionAmount = 0 AND invoice &gt; 0) THEN 1 ELSE 0 END) AS 'September No Deduction', 
    MAX(CASE WHEN (PayrollDeductionMonth = 'September' AND PayrollDeductionAmount &gt; 0 AND invoice = 0) THEN 1 ELSE 0 END) AS 'September No Invoice', 
    SUM(CASE WHEN PayrollDeductionMonth = 'October' THEN Variance ELSE 0 END) AS October,
    MAX(CASE WHEN (PayrollDeductionMonth = 'October' AND PayrollDeductionAmount = 0 AND invoice &gt; 0) THEN 1 ELSE 0 END) AS 'October No Deduction',
    MAX(CASE WHEN (PayrollDeductionMonth = 'October' AND PayrollDeductionAmount &gt; 0 AND invoice = 0) THEN 1 ELSE 0 END) AS 'October No Invoice',
    SUM(CASE WHEN PayrollDeductionMonth = 'November' THEN Variance ELSE 0 END) AS November,
    MAX(CASE WHEN (PayrollDeductionMonth = 'November' AND PayrollDeductionAmount = 0 AND invoice &gt; 0) THEN 1 ELSE 0 END) AS 'November No Deduction',
    MAX(CASE WHEN (PayrollDeductionMonth = 'November' AND PayrollDeductionAmount &gt; 0 AND invoice = 0) THEN 1 ELSE 0 END) AS 'November No Invoice',
    SUM(CASE WHEN PayrollDeductionMonth = 'December' THEN Variance ELSE 0 END) AS December,
    MAX(CASE WHEN (PayrollDeductionMonth = 'December' AND PayrollDeductionAmount = 0 AND invoice &gt; 0) THEN 1 ELSE 0 END) AS 'December No Deduction',
    MAX(CASE WHEN (PayrollDeductionMonth = 'December' AND PayrollDeductionAmount &gt; 0 AND invoice = 0) THEN 1 ELSE 0 END) AS 'December No Invoice', 
    Total 
FROM
    (SELECT
        PayrollpersonID,
        PayrollDeductionAmount,
        i.invoice,
        PayrollDeductionAmount-i.invoice as Variance, 
        PayrollDeductionMonth, 
        PayrollDeductionYear, 
        Total = sum(PayrollDeductionAmount -i.invoice) over (partition by PayrollpersonID)
    FROM
        Employee_Deductions as d, 
        (SELECT
        InvoicepersonID, 
        sum(isnull(v.InvoiceAmount,0.00)) as invoice, 
        InvoiceProcessedMonth, 
        InvoiceProcessedYear 
        FROM 
            Employee_Invoices as v
        WHERE DeductionYear = '2015' 
        GROUP BY InvoicepersonID, InvoiceProcessedMonth, InvoiceProcessedYear) as i
    WHERE
        d.PayrollpersonID = i.InvoicepersonID and 
        d.PayrollDeductionMonth = i.InvoiceProcessedMonth and 
        d.PayrollDeductionYear = i.InvoiceProcessedYear and 
        d.PayrollDeductionYear = '2015' and 
        d.PayrollDeductionAmount &gt; 0) AS a
GROUP BY PayrollpersonID, 
    PayrollDeductionYear,
    Total
ORDER BY PayrollpersonID;


You could have done this by stacking pivot statements but this can be messy and inefficient. This is a different way of pivoting data called the cross tab method. This method is usually more efficient than the pivot statement and easier to read.