Partial Online Payments

What is the best way to handle partial online payments?

Here is what I would like to do:

1. Send client an invoice for the project before the project begins.

2. Client pays 50% of project upfront using the online Paypal payment option in the email that they receive.

3. I record the partial payment in Zoho Invoice.

4. At the end of the project I send the client an updated version of the invoice that reflects their 50% payment and the 50% still owed.

5. Zoho automatically reminds the client of the remaining balance at set intervals, based on the date the invoice was sent at the end of the project, until invoice is paid in full.

Now here are the problems I'm having with the above workflow:

- It doesn't appear that Paypal allows the client to make a partial payment. Does Google Checkout?

- Zoho sees the initial date of the invoice as the date to start counting down the net terms, so the client starts receiving reminders for remaining payment that is not even due yet because the project is incomplete.

Can you help with any ideas to make the above work without needing to generate two separate invoices?

Thanks!