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The following procedure can be followed to apply a partial payment to an invoice:
Alternatively, if you know before hand that a client is planning on making payment for an invoice in two or more installments. e.g. 50% immediately, 50% in 30 days. You can create two separate invoices each containing 50% of the original quote amount and mark each as paid when payment is received.
SnapBill does not currently have a complete partial application of payment to invoices feature. We have a ticket open on our development board for the implementation of such a feature.
New features are pushed into development according to the amount of user interest they receive on our development board. If you like this idea then please put your vote behind it or comment on it here: https://trello.com/card/process-payments-partial-payment-application-to-invoices/4ef03eb6ca6b549007460e01/12.