Go into the job that you would like to take a partial payment on and click on Pay.
You will then get to the screen with the amount of the invoice. You will be able to click on the amount and edit how much you would like to apply, add a note and also be able to see if there have been payments applied on the invoice already.
NOTE: you cannot apply a payment that would exceed the total amount.
You will then hit the right arrow to choose the payment method.