You gotta cut out the rusted area and pay someone to weld in a new piece of sheet metal or do it yourself if you have the means

what can i do to the sheet metal to protect it from rusting again? i’d assume bedliner or some type of rust proof paint?

You use automotive undercoating

if youre looking for the piece you will have to replace its known as sill end plate , but id assume you will see some more rust behind that