I put bed liner (cheap stuff) on one of my flat deck truck under my water/fertilzer tank. NEVER AGAIN. The moisture/fertilzer got under it where it wore and made a mess and it was on a fresh new deck. When I put a new deck on my second truck, I did nothing. It had some minor surface rust where the tank rubbed. A wire brush cleaned it up and I rolled on some fresh paint. I do this every fall when I put the trucks away now. Blow the loose paint off and it dries. You don't notice it at first with bed liner, but when you do, it's too late. Years a go I had a deck painted with a heavy duty 2 part epoxy paint, it was tough as hell, but again once it got a scratch in it to the metal, moisture got under it and ate it away while it just bubbled up and festered. The deck was just rotten when I replaced it. The epoxy paint and bed liner just held the moisture and it ate the decks. The decks I had with cheap paint, the paint would blow off and it would dry and I would get some minor surface rust and I would touch it up. The under coated and epoxy decks took a beating and just rotted. It only happened where there was a cut or scratch for it to start or on a seam like across the front of the bed. I took off as much as I can on the one I did, hopefully it won't get much worse and it was new 3 years ago.
My paints holding up all over, but in time if I had to do something, I would clean it up and just spray flat black under my fenders and touch it up if needed.