Customer advance invoice function from projects should work the same way as Vendor invoice prepayments work on AP. so a prepayment posting profile can be used to separate ledger entries, also and in addition allow for a different posting layer (similar to tax and fixed assets). Some countries do not want the prepayment invoice to create ledger entries when the invoice is created and only want the ledger updated at time of payment applied to the pre-payment invoice, but they still need to track/report the "liability" created. They must be able to create the required prepayment separate from the Project sales orders, it must be reflected on the project so they can link the prepayment invoice to future project sales orders or invoices created for the project.
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