The total fees for your goods or works/services is $500. You collect a deposit of $100 to start and the balance of $400 will be collected when you complete the works/ services or deliver your goods. There are a many ways to handle this. Here are 2 suggestions :
Option 1 : Issue One Invoice for $500/-
At the time the customer orders, prepare one invoice for the full amount. In the amount column, ensure that the total amount is $500. In the description column enter text to indicate that a deposit of $100 is required to place an order or to start work. The balance of $400 is due on completion on delivery. The total invoice amount will still indicate $500. When customer pays the deposit, apply $100 payment to the invoice. When goods are delivered or service is completed and customer pays the balance, apply the remaining balance payment of $400 to this invoice so it is paid in full.
If you report sales tax on an accrual basis, this method also has tax, sales and profit implications as you would need to report on the tax collected for the full amount of $500. It also has implications on your sales and net profit since the balance amount may not be due for sometime. So this method is typically more suited where the time frame at the time of deposit to time of completion is short, say a few day.
OPTION 2 : Issue one invoice for the deposit of $100 and another invoice when balance $400 is due.
In this method, you will need to issue 2 invoices. For the customer to confirm their order, you issue one for the deposit of $100. In this invoice, you will indicate in the description column that this is just a deposit payment for the total amount of $500. The invoice total will still be $100. Then when work is complete or you deliver your goods, you will prepare your final invoice of $400.
This method is typically used for project or contract work where it may be a while from the time you start work or order is confirmed to the time you complete the work and final payment is due. This method may more accurately account for your sales, net profit and sales tax. You can use this method for progress billing as well where you invoice the customer based on the progress of work completed.
If you are unsure on how to handle this, you should seek advice from your Accountant.