1. Turn on progress invoicing. Go to the gear icon, then Account and Settings > Sales, find the Progress Invoicing section, and switch on "Create multiple partial invoices from a single estimate." Save.
2. Create the estimate like normal. Build the full-project estimate the way you'd build any other, every line item and the total amount the whole job is worth.
3. Get it accepted. Mark the estimate Accepted once the customer signs off; progress invoicing works from accepted estimates specifically.
4. Convert it to the first invoice. From Sales transactions, open the estimate and select Convert to invoice. Choose how to split this round: a percentage of the whole estimate, specific line items billed in full, or a custom amount per line.
5. Let QuickBooks track what's left. Each progress invoice shows what's already been billed against the estimate and what's still remaining, so you're not manually subtracting to work out what's left to invoice.
6. Repeat at each stage until the estimate is fully invoiced. Convert the same estimate again at the next milestone, picking up where the last invoice left off, until 100% of it has been billed.