To generate a document that indicates the amount you would like to get paid in advance, click the Print button and choose Advance Invoice from the Document Type menu.  You'll be prompted to enter an amount.  The amount entered by default is the percentage indicated in the Estimate Terms section of your preferences.  

Once printed, Blinkbid remembers this amount.  When you transfer your estimate to the invoice you'll be asked if you want to add the advance amount as a payment in the invoice.