"These payments are not made from the business account. Therefore, payroll can't be instructed until the final payment is made by the owner."

It's still only problematic across the year end.

First, most people know what the upcoming payment will be.

Second, payroll processing usually waits for all submissions that affect year end, including health, allowances, taxable fringe such as transportation and tuition, etc.

Third, even if the person has a final late Dec payment that they pay personally, and they don't submit that to be reimbursed until Jan, you put it on the Jan paycheck. Paychecks are not accrual.

"and I'm refining how to talk with owners about this area of tax."

What you might not have is people familiar with being responsible for their own payroll timeliness? Which is why they can use someone, outsource to ADP or a local CPA office which offers payroll services. At least until your client gets up to speed.

Here's a comment I use often: If you are an engineer, you have better things to do than stand at the Kinko's copiers. Let your clerk do that part; your time is more valuable by doing your engineering.

The same is true for payroll. Don't do your own payroll when your business skills give you a higher and better use of that time.