Bed board underside treatment
 

I used deck seal on both my flatbeds, top, sides, ends and bottoms.

I just used the same poly coat as on the top. Something smooth and non-porous is best, because it makes it easy to wipe off the grease slung by the u-joints, and any 90wt that gets by the pinion seal.
https://cimg8.ibsrv.net/gimg/www.for...96a81ccf76.jpg

The underside has to be protected as good as the top. But don't forget the sides. And after you drill your holes try to get the sides of the holes treated.

When I did my boards in 1999 I gave the bottoms the same number of coats of spar varnish as the top. I redid the boards in 2016. I sanded them to bare wood. I had to replace two boards. I then painted them with 3 coats of oil based paint, that matches my meadow green perfectly, tops, bottoms, sides.

Before you drill your holes maybe you ought to lay the boards I the bed to be sure they will match your bolt holes on your bed sides and the hold down bolts.

I used POR-15 and then painted over the POR-15. Created a nice surface that protects the wood.

I painted the boards from both sides with the same paint. Since I don't expect to drive the truck in foul weather this should be sufficient. I didn't drill the holes into the boards before installing them but afterwards from below the truck with a long drill. That way You don't need to measure all the point which may or may not fit in the end. But be careful when drilling from bottom upward. Use high RPM but low pressure on the drill. That prevents splinters when the drill comes through the surface on top. In addition, You can put transparent tape on the area where the drill will brake through.

BJ it is best to put the same number of coats as the top sides. You can always put undercoat on too, but you want the wood sealed on all surfaces, edges, and ends.

Abe is right about coating the underside as good as the topside. Although you don't have to worry about UV deterioration the underside does get a lot of road-blast which is rarely cleaned off. Years ago I had used a temporary flooring of marine grade plywood. When I pulled it off I was surprised at the amount of deterioration underneath despite very little use. That is one of the reasons that I went with TREX covered with polished AL diamond plate.
https://cimg4.ibsrv.net/gimg/www.for...5e9dc3c9a0.jpg

Plus don't forget to coat the inside of the holes you drill for the mounting bolts. These are the products I used on mine (four coats) , My truck also sees very little weather exposure.https://cimg2.ibsrv.net/gimg/www.for...e1afb70e05.jpg

:-hijacked
For those who haven't decided what wood to use and don't ever want to replace it again you can use Accoya. It has a 50 year guarantee against rot. You don't have to finish it at all if you don't want to and it doesn't shrink or expand. I found out about it when a client wanted me to build him a Japanese soaking tub. He has had the tub for 5 years now and says that he uses it several times a week. Since I have made outdoor children's play furniture for a church pre-school, several other outdoor projects, and the bed on my F1 flatbed. They can make Accoya out of many woods, what is available is either Radiata Pine or Alder. It has been used in Europe for years on many outdoor sculptures and buildings. https://www.accoya.com/faqs/

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Selection of the proper wood is just as much of an importance as the finish used. Some of the most Rot resistant woods are Black Locust, Osage orange ,( think farmers hedgerows and fence posts), teak , ipe , California redwood , and bald cypress. Except for two ( Teak and Ipe) most are available in North American regions. If Oak is used, White Oak is a preferred because of it's unique cell structure as opposed to Red Oak. A thorough soaking of all surfaces is best with a solution of your choice and can withstand the climate and exposure .
I read some time ago that when Henry Ford installed wood in the beds that Coal Black and Linseed Oil where used as the finish so considering that we've come a long way in our own choices of wood products for our builds.