Quickbooks Desktop version allows you to do what's called Progress Invoicing. This makes a lot of sense for what we do. You can make an estimate for $10,000, then do 4 invoices - one each for $2,500 and it will track the invoicing progress showing you how much work was estimated and invoiced to date.
Unfortunately, Quickbooks Online doesn't appear to have this functionality. You can only create 1 invoice per estimate and as soon as you make an invoice (for any amount) from an invoice, QBO automatically marks that estimate as closed - even though it was not fully invoiced.
You can workaround this issue by manually marking the estimate as PENDING again, then creating another invoice from it. This action, however, clears the link to the first invoice, so you'll never be able to track multiple invoices to one estimate.
For more questions or to make a suggestion to Quickbooks to bring back the ability to do progress invoicing against estimates, contact their support/suggestion department here: