Sale Orders are layaways.
A Sale Order is a layaway - it provides a balance to be paid toward, it holds the inventory but does not deliver it to the customer, and it does not show as a finalized invoice (taxable income) until you manually tell it to become one. This function was developed for government contracts but works great as a standard customer layaway system as well.
From an accounting and reporting standpoint, you will be seeing monies received only for the actual funds that come through and no final sales, just deposits. Once the sale order is converted to a final sale, all funds transfer from (non taxable) deposits to (taxable income) sales on your sales tax reports and in Quickbooks. Sales tax is pre-calculated for the sale order so all is paid for.
When a sale order is created all related inventory will be held in a special status -- unlike a quote, which does not remove inventory from quantity available -- but a sale order does NOT show the items as having been delivered to the customer.
You will see in your inventory area that you have a "held for SO" column. These items will not be available to sell to other customers, but also have not yet been removed from your inventory assets pool until the sale is finalized.
See related article "Create, Edit, and Close Sale Orders (Layaways)" for instructions on use.