Per the discussion below, would I write a check to Employee or Vendor in this case?

Create a check for the employee.

To pay the employee, see the following options:

Create a regular check:

1. From the Banking menu, choose Write Checks.
2. Enter the date as the date of the original paycheck.
3. On the check, in Pay to the Order of, select the employee for whom to issue the check.
4. In the $ (amount) field, enter the net amount of the direct deposit.
5. On the Expenses tab, in the Account column, select Direct Deposit Liabilities. (Select Cancel if prompted to pay payroll liabilities.)
6. Check the Print Later box at the top of the page, next to the Print icon.
7. Select Save & Close. Since this is a paper check, it does not need to be transmitted to Intuit.