Not everybody pays by Direct Debit. A payment made any other way is recorded here and counts exactly the same.
Otherwise you would be keeping a second list beside this one, which is not really having your subs on one screen.
Marking somebody as paid
Open the member on the Money screen and say how they paid: bank transfer, cash, cheque, or something else with a note.
It writes the same record a Direct Debit writes. So the totals, the arrears list and the member's own record all agree, without anybody keeping a spreadsheet alongside.
Nothing about this touches GoCardless, and nothing here can. It is your club saying money arrived.
Waiving a sub
Sometimes the club decides somebody does not owe it. An honorary member, a hardship case, somebody who joined and then could not play.
Waive is that answer, and it is not the same as marking them paid.
The sub still happened and the record still says so, with a reversing entry against it and your reason on it. What changes is that they are no longer in arrears.
Waiving twice posts one entry, not two.
Paid status where you actually look
Whether somebody has paid shows beside their name on the box rosters and on the ladder, not only on the money screen.
The register and the leagues are one list rather than two. So whoever runs Tuesday's boxes can see it without asking the treasurer.
Who can see the money at all is a permission of its own: the treasurer and the owner by default. See Who does what.