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There are Three Payment Method
X----------AE Direct Deposit AED(Type)
all above payment Method have different Cash Clearing Account in General Ledger Tab
When I run the Post Payroll Process (Cash, Cheque Writer (generic)and Transfer to GL) then in GL Module Transfer only one cash clearing account hit which is define in Y
while in personal Payment Method of employee assignment is define X Payment Method so I want that in GL Module hit the cash Clearing account of X not Y.
Not sure if this is helpful.
After you run the prepayments process, could you check the payroll process results (from View -> Payroll Process Results in your hrms responsibility) for each assignment to see if the status is Paid or Unpaid. Typically you will run - payroll run, prepayment, cash, check, magnetic transfer (or whatever is used for your legislation), costing and transfer to gl.
running prepayment alone will leave the payment status for the assignment as unpaid. When you run the cash process, everyone with a cash payment method attached should have a status of Paid. So there are processes for employees with cheque payment method and direct deposit as well.