In the Admin Dashboard, click on the student's name from the Students tab. Click on the Payments tab at the top and then click on the "Add payment" drop-down menu. Click "Charge payment method"

The Create a new payment screen will appear where you can enter all payment details such as:

Select the checkbox near "Save as a new item on statement" if you would like for this payment to also create a new charge at the same time. The payment made will go towards any existing charges first and then towards the new charge/item created. If unchecked, the payment will pay off an existing balance.

You'll notice in the example below, a new May Tuition debit for $1000 was created. There is also a payment on the Credits tab for the same amount. The payment made here is first going to pay off Marlene's $1000 existing balance.