Customer prepayments for inventory items

"When our accountant invoices the items on the sales order for the prepayment, the items are immediately subtracted from inventory and drive it to a negative inventory. "

Yes, that is done using an Other Charge type item, not the actual inventory item.

"Just go to Customers -> Receive payments. Enter amount and in the lower left corner click "remain as available credit". "

That creates negative AR and is not a good process to use holding this for any length of time.

You want this method, for the prepayment:

https://support.quickbooks.intuit.com/support/pages/inproducthelp/core/qb2k12/contentpackage/core/re...

And this for the application of the prepayment to the final/actual gross charges:

http://support.quickbooks.intuit.com/support/Articles/HOW12869

a sales order is non-posting and does not change inventory.  receive the payment from the customer and do not apply it to an invoice.  it resides as a credit on the customer account.  when the build is complete and you're ready to ship, invoice the total amount and apply the credit to the invoice.  the customer will owe you the balance.

I met with a customer yesterday also dealing with customer deposits.  Her customers want "receipts", so posting the paying and leaving a credit will not suffice.  My best resolution is to create a Customer Deposit Account in current liabilities, then set up a Customer Deposit item that hits the account.  You invoice customer for deposit, then apply deposit received on a later invoice and it backs it out of the liability account.  The liability account also makes a very nice list of who you have deposits from if keep the account reconciled to zero.  Do not use sales receipts for this - they don't show up on customer statements.  The tricky part is remembering to apply the deposit, because QB isn't going to do it for you.  Also, using the Memo at the bottom for "Deposit Request" on invoice and "Deposit Received" on payments make nice neat notes on the statements.

I met with a customer yesterday also dealing with customer deposits.  Her customers want receipts, so posting the paying and leaving a credit will not suffice.  My best resolution is to create a Customer Deposit Account in current liabilities, then set up a Customer Deposit item that hits the account.  You invoice customer for deposit, then apply deposit received on a later invoice and it backs it out of the liability account.  The liability account also makes a very nice list of who you have deposits from if keep the account reconciled to zero.  Do not use sales receipts for this - they don't show up on customer statements.  The tricky part is remembering to apply the deposit, because QB isn't going to do it for you.  Also, using the Memo at the bottom for Deposit Request on invoice and Deposit Received on payments make nice neat notes on the statements.