We often bill jobs based on a percent of work completed OR based on certain items being completed. If we have a $12,000 job, we will bill a $4k deposit, a 4k progress invoice and $4k on final. Alternatively, we might have 20,000 Sq. Ft. of work to do but it's being completed in phases. So we might bill out 60% of the work as a progress invoice and bill the remaining work upon completion.
It would also be extremely beneficial to allow change orders to be added as a new "section" on the estimate and allow this to flow through to Quickbooks. Also, section headers don't flow through to QB which is problematic since the information is not reflected accurately in both QB and JN.