Mmm, whether I paid the vendor directly or the employee, the account that the check pays from was still going to be my regular business checking account, so that stays the same. And the expense for the bill is still going to be whatever it would have been normally (Office Supplies in my case), so the expense account can stay the same, too, no payroll accounts would or should be involved.

It sounds like you might be trying to get the reimbursement included on their normal paycheck? In which case, yes, it'll be a lot more complicated to make things balance.