Like the others here, I plug in every number from my pay stub.
Doing so allows you to break down exactly how much tax you
are paying, the amounts of pre or post tax deductions, etc.  An
example w/o the numbers:

2012-02-06 Stanford University Paycheck
        Assets:USAA:Checking                           $_,___.__
        Assets:403b:SCRP                                 $___.__  ; 403b: 
employer basic
        Assets:403b:SCRP                                 $___.__  ; 403b: 
employer match
        Assets:403b:SCRP                                 $___.__  ; 403b: 
pre-tax
        Assets:403b:SCRP                                 $___.__  ; 403b: 
post-tax
        Expenses:Tax:Federal:Withholding               $_,___.__
        Expenses:Tax:Federal:MED/EE                       $__.__
        Expenses:Tax:Federal:OASDI/EE                    $___.__
        Expenses:Tax:Ca:Dis/EE                            $__.__
        Expenses:Tax:Ca:Withholding                      $___.__
        Expenses:Insurance:Medical                        $__.__
        Expenses:Insurance:Vision                          $_.__
        Income:Stanford:Salary                        $-_,___.__
        Income:Stanford:Pager                           $-___.__
        Income:Stanford:SCRP:Basic                      $-___.__
        Income:Stanford:SCRP:Match                      $-___.__

The '; 403b:...' markers allow me to run a report like this:

  ledger bal 403b:SCRP --pivot=403b -b 2012 -e 2013

which will provide a report on employer, pre-tax, and post-tax
contributions to a 403(b) retirement fund (something in the
US that lets people save for retirement in leu of a pension,
but which has very specific rules about pre-tax and total
contribution limits).

Jim

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