The following procedure can be followed to apply a partial payment to an invoice:

• Apply the payment without marking any invoices as paid.
• In the reference box on the Process Payments screen add the invoice number the payment is in reference too to link the two.
• Once full payment is made for the invoice, process the second payment to mark the invoice as paid and the existing credit will automatically be applied to it.

Alternatively, if you know before hand that a client is planning on making payment for an invoice in two or more instalments. 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.