How to pay an employee from two different checking accounts
If necessary, set up a new pay data line in the pay data tab of the employee's record.
When processing payroll, remove the line for the item that will be paid with a different checking account: In step 3) Edit Timecards, click the red X to the left of the item to remove the line.
Continue to process payroll as normal. Then, create a new payroll, repeating the process to pay the amount that needs to be paid with a different checking account: select the appropriate checking account and remove the item(s) that should not be paid with the selected bank account.