Well, in this particular case the new (and lame) inability to set up two employee records for the same person is actually helping.
You shouldn't set up the same person twice in order to give them two paychecks per pay period from different bank accounts, and also for most any other case.
Doing so will cause all sorts of issues, including that as an employer the employer paid tax limits won't kick in and so you'll potentially pay way more tax than you need to pay. Up to 2x more. And also your employees will appear 2x on some state forms, and they'll get two W-2's. That and other similar things will no doubt cause various issues with the agencies you report to and for your employees.
Similarly, any employee paid payroll tax that has a limit may be exceeded over the year.
Also, creating two checks for one employee in a pay period will cause state and federal income tax withholding to be under-withheld when compared to the Employee's W-4. You are required to withhold the correct tax per pay period based on the W-4 each employee gives you, and creating to smaller checks for a period basically ensures that won't happen.
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Still, there is one way to do this properly - where the paycheck will calculate properly and where various down-stream issues will be avoided. This is to create one paycheck, but to reduce it and then create a second bank check - not a paycheck - for that amount. Then print both checks.
The trick to do this is to...
- Create a net deduction payroll item, with a tax tracking of None, which uses a liability account you created just for this case.
- Next, add the deduction to the employee records and, if you know the amount for the second bank account, you can specify an amount. Or enter 0.00.
- Then when creating paychecks, review the check detail and enter the amount for the other business account. (Say you're recording the paychecks in the School account, then enter the amount for the Church account.) This will reduce the net pay but have no effect on payroll reporting.
- Next, create standard checks in the Church account (in this example case) for those amounts, and for the "expense" account, enter the liability account. When done, the liability account balance will be 0.00, which is a good cross-check. The standard checks will have no impact on payroll reporting.
- Last, print both batches of checks for your employees.
