Progress Invoicing

Estimates are pending until they are closed, and they do not show up on an A/R Aging Report. You can convert an estimate into an Invoice, which would show up on an Aging Report until a payment is applied to it. If a progress invoice was created for which a deposit/retainer is on file, that deposit/retainer needs to be applied to the progress invoice to clear the balance off the A/R.

One more important detail to note. You need to "turn on" the ability to create multiple partial invoices from a single estimate. This can be turned on under "Account and Settings" / "Sales" / "Progress Invoicing".