Here's what I did:
1. Create a invoice for the full amount.
2. Manually charge his card at authnet for 50%.
3. Under Invoice, I went to the Add Payment tab and entered the gateway (authorize.net), amount, and transaction id from authnet. I also ticked the send email to client.
This seemed to be the only way I could figure out. It did NOT send an email to the client. I'm guessing because it was only partial payment, which seems weird since the default email is "Credit Card Payment Confirmation". and theoretically this is what I was hoping would be sent.
anyway, if there's an easier way to create one invoice and apply partial payment that would be great.
thanks,
Scott