When a customer prepays, it should be recorded as a liability because now you owe the customer something and you haven't really earned that money yet.
In the chart of accounts, create an Other current liability type account called customer prepayments or deposits or whatever makes sense to you.
In the item list, create an other charge or service type item called prepayment, deposit or whatever and use the account you created above. Make sure this item is not taxable.
If you need to invoice the customer for the prepayment that they will pay later (sometimes customers require an invoice for any payment), Enter an invoice using the prepayment item.
If they are giving you the money right now, then enter the transaction as a sales receipt, using the prepayment item.
Once the actual sales occurs and you want to apply the prepayment, do the invoice (or sales receipt) like normal for the full charges, then add the prepayment item for a negative amount to be applied and the amount owed on the invoice will be correct.
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