Here is how to make a partial payment on an invoice:
Step 1:
Open the invoice from the grid, locate the payment line in section 3 (Payment Schedule)
click on the arrow and select "Edit".
Adjust the amount to reflect the amount of the partial payment made by the customer
Click on "Pay"
Step 2: Enter the payment information in the "credit card" or "manual payment" window and save
Step 3: In order to see the balance of what remains to be paid on the payment schedule, click on "Add a payment".