Hi DigiRizz,
Here is the stock workflow today we have in terms of Deposits.
Currently, when an estimate is emailed with a set deposit amount, the customer accepts the estimate on the portal and pays the deposit amount. A sales receipt is created for the deposit amount. For example: 100$ = Estimate Amount, 50$ = Deposit Amount, When deposit paid - Sales Receipt Created = 50$.
When the Create Invoice button on the New/Edit Estimate Screen is used, it creates an Invoice for 100$, with a Deposit Paid line item added to the Invoice for -50$.
For the above, if you don't want to customize, you can ask your customers to make partial payments to the Invoice which has a balance due of 50$ now.
No link between estimates and invoices exists right now but can be customized and a grid can be shown on the New/Edit Estimate Screen to show all Invoices linked to that estimate.
However, you can connect the estimate and the invoices to the same opportunity to establish a link on the opportunity level - but this is a workaround.
If you want help achieving this we have an in-house customization team who can help you with this(billable service), so they can select the amount they want to pay/invoice.
Cheers,
Inder