Unfortunately, this isn't how it used to be on our old site where you could enter the amount you wanted to pay into a textbox. Now you get to do math! Fun.
All you have to do is add the amount of money you wish to pay towards your order to your shopping cart. For example: If I want to pay $250 towards my RN-50 I would add $200 to my cart once, click "continue shopping", and then add $50 to my cart once. Then checkout.
Please include your order number or make sure to have all contact info provided so I know whose order to apply the payment to.
It's a roundabout way of doing things, but for now - in the spirit of getting the website back up and running - this is the quickest way I could do so as there is no application for it through BigCommerce.