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Is there any way of paying a proforma invoice for a deposit and leaving that payment on account and marking it to not be included in any future payment runs?

Hello-

 

If you utilize the supplier payment proposal, you should be able to add a line to the pay proposal referencing a payment in advance for the amount and supplier.   It would require a manual intervention when the actual invoice arrives to offset the amount initially paid against the remaining installment due.

 

I hope this helps.

 

Best-

Christy