Yes, if a deposit has been taken for a booking, it will automatically appear as a deposit being redeemed agains the total value of the client's booking, displaying the total remaining to pay at the bottom of the screen, like so:
However, if your client prefers not to use their deposit as part payment for their booking, and instead leave some (or all) of their credit on balance, you can adjust the amount in the "Enter deposit amount" box to whatever the client prefers.
Any remaining credit that is not redeemed in this bill will remain on the client's account, being visible in Outstanding Deposits, and redeemable against another booking by using the Search Deposits function in Checkout:
Click on "Deposits"
Click in the box to start and start typing the client's name to search for them:
Select the client:
Then enter the deposit amount your client would like to redeem against the bill and this will be automatically knocked off their total: