Upon checking and testing, there is no built-in option yet for changing the order of fields for the sublist type that the Apply sublist falls under. The following related Enhancement Request has been filed for a possibility of future implementation:
Enhancement 174078: Transactions > Customers > Accept Customer Payments > Apply > Invoices > Ability to move and/or remove the default Columns
you should have a User Event Script on Before Load to hide the appropriate fields.
it appears that hiding sublist fields can be only done using User Event Scripts at the moment. So, I retract the client script part in my previous answer. The following related Enhancement Request has been filed for a possibility of future implementation:
Enhancement 254142: API to hide/unhide Sublist fields in client-side/browser