How to bill the client incase of advance recieved?

Kindly guide in the following situation The organization charges clients for the logistics services. The clients pay part payment in advance and balance payment on the safe delivery of goods. Now the question that I’m facing is that while billing the clients for freight charges, should I charge the company for the full freight payment or should I adjust the advance in the bill. If I follow the adjustment in the bill approach, that will indeed reduce the bill amount and hence my sale. How should I raise the bill to the client? Looking forward to the valuable inputs Thanks in advance