When your customer goes to the checkout page, you can choose the order in which the payment methods appear.
Head to your Customer Area and click Account > Checkout Settings and define the order of the payment methods that will be shown to the shopper.
If you cannot see the Checkout link, contact our Support as you may be missing the necessary permissions.
Unfortunately there is no way to sort payment methods on the Pay by Link page right now. The order of the methods is normally based on the countryCode that was sent in the request, or the IP of the shopper.