What is recommended when doing a spray in bed liner like Line-X, remove the plastic bed trim caps and spray over the rail leaving the bed rail caps off?? Or leave them on and spray up to the caps?

It's really up to you. I don't have bed caps on my truck so when I get my liner, I'm having it done over the rails.

Its up to you. I would leave them on and just go up to the caps. I don't have the caps on the bedrails so I will be and have done in the past, over the bedrails. However there is the plastic cap on the tailgate. I have left that and just go up to that and it looks and performs great.

there are holes under the rear factory cap so dont take it off

Speaking from experience, I would leave them on. Both the Rhino Lining and Line X will absolutely fade so if you spray on the bedrails eventually that will look faded and old whereas the cap will always look glossy.

I went over the rails on mine with Line-X. There is an extra chemical they can put in the Line-X to keep it shiny. I got it on my last truck but it's like another $100 extra. This time, the Line-x guy told me it wasn't necessary and gave me a bottle of conditioner/UV blocker and a sponge applicator. When it starts to fade, just wipe it on and it will look like new again.

If you have the factory plastic rail caps, keep them on and have the bedliner applied up to the caps.

If you get LINE-X, opt for either Ultra Shield, Nason, or LINE-X Xtra. All are one-time applications and will prevent the loss of gloss and fading.

If you can keep it from fading, I think it would look good to have it up on the bedrails.

If you take the plastic off, you will see that the rail is not very nice looking. In addition, the holes are a problem. Ford, Chevy, and Toyota all have the holes.

http://img.photobucket.com/albums/v413/123Gone/fordholes.jpg

To the rails.