It's vital that all your transactions are correctly entered for your books to be well balanced. QuickBooks Online is a great tool able to help you send sales forms such as estimates and invoices to your customers. I can point you in the right direction to enter your invoices.
When creating an invoice from an estimate in the mobile app, the only option would be to create an invoice for the whole amount of the estimate. If you'd like to use the progressive invoicing feature to invoice only a part of the estimate to the customer, the invoice would need to be created by logging into QuickBooks from a browser. I can see that having the ability to create partial invoices for the estimate would e a feature that you'd like to see available on the mobile app. I recommend you leave feedback in the system for the developers by clicking on the Gear Icon, then Feedback. The comments made in that section are taken into consideration when designing new features for QuickBooks Online.
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