Help on creating Invoices

Our current invoicing is as follows:
- Architectural fees for a project are a pre-agreed fixed amount - the contract amount. Our contracts are the result of an offer (estimate) sent and agreed by the customer
- The project is broken in 12-15 work stages each of which bears a % of the contract amount e.g stage 1 - deposit 10% of contract amount, stage 2 - design 15% of contract amount etc
- At the completion of each stage the client is billed with the corresponding stage amount, (based on the stage %)
- More than one stages can be billed together

On the invoice we would like the following to appear
- Contract Amount
- % of work completed up to the billing date and corresponding amount (Amount 1)
- Previous customer payments for the specific project - automatically calculated from previous payments made by the customer for the project (Amount 2)
- Current invoice amount due (amount 1 - amount 2).
- VAT
- Total Amount due

Is there a way to create such invoices through Zoho Invoice?

Thanks
P.S. I have tried setting up each stage as a different invoice for the customer but they are treated as standalone invoices (e,g, if customer pays more it does not automatically transfer the excess to the next unpaid invoice).
I have also tried setting up an estimate with tasks and invoicing it progressively but again it does not provide me with the customer's previous payments on the estimate.
Perhaps I can do this via automation?

Thanks