Progress Invoicing should be drawing from the estimates Tab not items tab. When I build me Estimate. I should be putting the payment Schedule into the Estimate. The Payment Schedule should not be set in stone by dates. Projects Change on the fly all the time and progress invoices have to be adjusted as progress is made. Quick books does progress invoicing properly. Each invoice should show an invoicing summary starting from the quote your pulling the invoices from.
For additional Estimates - We Label these as Extras or Changes Numerically. Again this extras or changes are little subsidiary tasks that must be signed off like the original quotation and invoiced as progress is completed .
Progress invoicing on projects may look like :
Deposit 20%
Rough ins 40%
Service and Distribution 25%
Final Finishes 15%