This can be found in the backend of Shopify -> Themes -> Actions -> Edit Codes -> Cart-Template.Liquid

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Number 1: Secure Checkout Buttons

Number 2: Any Additional Payment Buttons, mainly Paypal, Amazon, Shop Pay and etc.

But if you wish to completely get rid of the buttons above or below then remove the #1 and #2. :)

Upper Buttons: http://prntscr.com/s6r1mk ( the order is #1 and #2 )

Lower Buttons: http://prntscr.com/s6r58a ( the order is changed #1 is #2 and #2 is #1 )

IF you wish to display the additional payment in the bottom, just get rid of the upper buttons completely and it will display at the lower part (vice versa)

Note: You can only choose to display one set of additional payment buttons either at the upper side or the lower side, you can choose both.