You should  first enter the original deposit in the sales journal except the account you would make the entry to is a liability account called customer deposits. ( as technically this is not a sale yet it is a deposit towards something)  Then you could enter the sales order as normal  with a total amount  of the sales on it and then on the last entry of your order you could put a minus amount and the account number would be the liability account called  customer deposits( this takes out the amount you entered when you originally received the deposit) . So if the sales order is for 4000 and the customer gave you a 1000 deposit than you would have sales amount of 4000 and then a line below (that in description you would type Less Deposit ) you would put   in a minus figure  -1000 so the total of the invoice would be 3000.  Hope this helps