There are two different transactions for each paycheck.  First you need to do the timesheet.  So using my paycheck as an example, you open up the recurring transaction called "Timesheet - Purser" in QuickBooks.  The date for this entry should be the last day of the pay period, so in this example it is 3/31/13.  The first three rows of the entry  should have numbers in the Debit column and the rest should have numbers in the Credit column when you're done.  The two columns should sum to the same number as well.  The top row of the excel spreadsheet tells you where in the entry to put the number in that column.  Keep in mind Columns I and J go in twice, once as a debit and once as a credit.

Once you're done with that entry, you open the "Paycheck - Purser" recurring transaction.  Fill in the current date and the check number.  The amount is the number in column H on the payroll spreadsheet.  It gets allocated fully to Payroll Payable in QuickBooks.  Obviously, this is when you write the actual check as well.