Right now you can only consolidate payment to the top level customer or parent customer. If you create a sales order for the sub customer then the invoice will also be for the sub customer. The feature to accommodate consolidation of invoice to the parent customer for sales orders created for sub customers is covered by Enhancement 97339 - Create one invoice to parent customer for multiple sub customers' sales orders.
An alternate solution for this is to use project or job instead of sub customers.
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