You might have figured this out on your own by now but the best way is to apply payments to open invoices and put them in undeposited funds. After that you can pull them into the deposit or after you've created the entire deposit, go back and the applied payment will magically appear in the deposit. Then you select it to add and just delete the original line that allowed you to match and save the deposit. There might be a quicker way but this is how I got it to work.