webpromo,
We currently have a request in our system to support this. It is a very large project as it would require a change in the way payments, clients, and invoices are linked together. It's definitely on our radar and we'll make note that you are interested in it.
With the current version, you could handle it by creating a $0 invoice, adding the payment to it and then adding line items to it as you render services to your client. If you have an invoice end up with a positive balance, you will need to transfer that balance or record that balance on the next invoice manually. One option would be to create a new payment type to add it to the new invoice.
If you would be interested in having us custom develop this piece for you, please email us at support@dotnetinvoice.com.
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Jeremy
DotNetInvoice Support