I went through this process on my build a few months back. We custom built white oak bed wood and coated it with Epiphanes brand marine spar varnish. I made that choice after a lot of research and looking through the Mar-K testing. My truck is garage-kept, so there aren't as many concerns about durability. We put 6 coats of the varnish on both the top and bottom of the boards. The process took about 2 weeks, since each coat needs to dry 24 hours before sanding and re-coating. I couldn't be happier with how it turned out. It seems incredibly durable and looks great. Only time will tell how it lasts. I certainly don't have the experience as others on here, but the Epiphanes varnish has a very good reputation as one of the best available.
Here's a picture of how it turned out. I still need to post some updated pictures.
As for the installation of the wood, there are a few things I would have done differently. I'll absolutely second everyone's mention of installing the wood with the bed off. It makes it so much easier. When I started installing the boards, i started in the middle of the bed and worked towards the edge. I ran into trouble as I got to the outside boards though. If I had it to do over again, I would have installed both of the outside boards, making sure the bedsides are in the correct position. On these trucks, the bedsides have a ton of movement/adjustability, so they aren't necessarily going to be in the correct position as they sit. If you install the outside boards and bolt them up to the bedside, you can adjust the board and bedside until they are lined up with the holes in the front panel of the bed as well as the holes in the support crossbars, the rest of the boards should fall into place pretty easily.
Finally, don't try to do this alone. It helps a TON to have someone in the bed holding down the bolts as you go.
Good luck, and let us know how it goes!