Yes, I do this already but that's not my question.  

I invoice my customer by progress from the estimate.  I go to Customer, create invoice, and it shows available estimates.  I click the estimate I am using to create an invoice, then click the 3rd option crate invoice for selected items or for difference percentage for each item.  I use the percentage.  When I click enter, it also opens a box that asked if I want to include BILLABLE TIME/COSTS.  I am using PERCENTAGE.  The issue is, Percentage does not change the VENDOR BILL to being billed.  When you enter a VENDOR BILL, you click the Billable box.  If you don't enter the VENDOR BILL on the CUSTOMER INVOICE using the BILLABLE/TIME COSTS, how do you know it has been billed?  I don't know how else to explain this.  I bill client by % but that does not change the vendor bill to being billed.