When I prepare a quote or estimate, it is for the entire job. Often, the jobs are billed in stages. The only options right now are to convert a quote or estimate to an invoice and bill the whole thing, edit the newly created invoice for the first progress bill, then create new invoices for future bills, or forget about converting and just do up new invoices each time. Whichever way it goes, the tracking on quoted jobs just doesn't work.
This really should tie in to the analysis type projects, and allow users to create a quote/estimate for a job, then create invoices for the progress bills and see how they balance out against the original quote.
At the very least, we should be able to split the quote or estimate into multiple smaller invoices.