Is it possible to accept partial payment by Square or PayPal?

I connected my form with Square for payment collection. However, is it possible to set a percentage of the payment to be collected? 

For example, customers make a pre-order and pay a certain percentage as a secured deposit?

Unfortunately, that is not possible. The products can be only paid at once, or at a later time: https://www.jotform.com/help/292-How-to-Enable-Payment-Authorization, but it is not possible to pay just a percentage of the total amount.