Yes, you will be able to do so as long as the Estimating program has a QuickBooks interface and you can bring the Estimate into QuickBooks and remove any subtotal lines from that estimate once it has been brought into QuickBooks.
If the Estimating program does not have a QuickBooks interface, you will need to create/duplicate the Estimate from the program using the QuickBooks Estimate form and your Item list.
As part of our testing, we created a very detailed Estimate using Craftsman National Estimator and used the Job cost Wizard to export it to QuickBooks. Once the Estimate was in QuickBooks, we simply deleted the subtotal lines, created Progress Invoices, and pulled them into Construction Application for Payment Solution; everything worked perfectly.
We have customers who are using Litening Fast, ProEst, UDA, and have tested Builders Software Enterprises.