Thanks @ShiellaGraceA. Shouldn't I use a pre-tax deduction since I would have already paid the tax on the extra amount given in the prior checks? I wouldn't want to be double taxed on the difference between the older checks and the current ones.

Example scenario:

• Original paycheck is for $1000/mo for as $12000 salary.
• New paycheck is for $800 for a $9600 salary.
• After 6 months, I've already paid my employee $6000, so he is due $3600 for the remaining 6 months.
• Quickbooks will create a check for $800 but I want to reduce it to $600 so that I'm not overpaying. I should add a pre-tax deduction to the $800 check reducing it to $600 since I already paid taxes on the $200 difference in the previous checks
  
  •  Alternatively, I could adjust the annual salary so that going forward, Quickbooks creates the $600 paycheck. I would then reset the salary to the desired amount at the end of the fiscal year. This option feels dirty though.