Thanks for updating this thread and sharing your concern with us, @cbsmith.

It's great to have you here, and I want to help you further.

The only time those charges in the Add Time/Costs is cleared is if it was assigned to a posting transaction. If you want to use progress invoicing and assign the other charges, create the invoice within the estimate itself at 100%. Then, once all the items are assigned to the sale, click the Add Time/Costs icon to add any additional charges for that customer.

Since you also need to create bills out of the estimate, the process of creating PO's from it is the correct process before bills. For now, can you please send some screenshots to show the duplicates you're referring to? This will help us make sure you're on the right track.

See this related link about the topic: Set up and send progress invoices in QuickBooks Desktop

If you have any questions or need further help with QuickBooks progress invoicing and billing, visit us anytime. You can also mention my name on your posts, and I'll be more than happy to help. Have a nice day!