If your talking about the plastic bed liners that you drop into the truck, I would be carefull.
All hitch manafacturs tell you to cut the liner and mount the rail solid on the bed.
I had 3 trucks with plastic bed liners and 5th wheel hitch. What I did was drill a 1" hole where the rail bolts pass through bed liner. I then used around 6 washers each bolt location so the rail was still solid mounted to the bed. This way the plastic liner could actualy move around in the space between the rail and bed metal. This required longer bolts be used for the rail to bed connectons.
in the new truck I have a spray in liner with the hitch rails sitting direct on top of it. If you go this way, install the hitch rails first, remove them, have the bed liner done, then open back up the holes and re-install the hitch. this way you can find any bed welds, etc that you need to align everything before you spray in the liner.