This was already set.  I have been able to invoice based on % of items, Line Items, or the other option since the beginning.

This is what I need:

Estimate = $1,000

Employee works 10 hours @ $25/hour billable

I add employee's time entries for project into invoice and the $250 is taken from the $1,000 estimate.

Leaving $750 left on estimate for next invoicing.