Hi there invoice3,
I appreciate you taking the time to go into detail about how your projects work outside of QuickBooks Online and what you're needing from the program in order to match those details. I can pick it up from here, highlighting how the different transactions in QuickBooks Online work while also directing you to a resource for some guidance with this situation.
You're right, estimates are not posting transactions, meaning that when you enter one into QuickBooks, the figures aren't recorded against your income, COGS, or reports. An estimate is just a placeholder to give your customer an idea of what their charges from you may be before sending on the invoice.
How the invoice tracks is going to depend on your accounting method in QuickBooks Online. If you're on an accrual method, you'll see the figures change on your sales reports and so forth. If you're on the cash accounting method, that only tracks real money received. In that case, you may also want to record the invoice payment if you're needing to show that the money has absolutely been received already.
As for recording income without an invoice, that's going to depend largely on your situation. Since you say the amounts are just for your records and to track alongside the expenses, entering invoices without payment may work for you. If you're simply wanting to enter money in, and it's actual money received from your customer, something like a deposit transaction may work.
Again, this is going to depend on your situation as well as how you're recording the other transactions for your project. For instance, if you're needing to show the that amounts are linked to an expense via a billable expense, then the deposit wouldn't work.
Then there's the matter of sending a single invoice at the end of the project. With your outline, it sounds like you've got something figured out that can work for you, which is great since there isn't a way to group together multiple invoices to form one master invoice. A workaround you can consider is keeping these invoices from along the way and then sending a customer statement at the end of the project so that the customer knows the grand total charge for your work. There won't be a way for them to pay via the statement, but they can know how much money to give you, then you can record the payment against the open invoices through the Receive Payments feature. Learn about those two features below.
Finally, if the features in QuickBooks Online aren't quite meeting your needs, you can consider a third-party project management service. A service like that may have more features you can work with to track and record your project transactions. Check out the Apps tab in QuickBooks Online and use keywords to search for these kinds of apps to learn what's available to you.
For this situation, I highly recommend speaking with an accountant to learn the best course of action for your books. Considering your knowledge when it comes to working with journal entries and moving funds that way, it sounds like you may be an accountant yourself, but if not, here's how you can connect with one using QuickBooks Online.
The My Accountant tab provides you with two options: the option to invite your accountant to your books as a user and the option of the Find a pro to help button to search and review QuickBooks-savvy accountants near you that you could work with. This is a great option for making sure you have someone on your side who can help navigate these kinds of complicated situations.
I hope this has been helpful. Here are a few articles about QuickBooks Online's Projects feature in case you'd like to take a look at how that works in more depth.