Tonneau and bed liner

I recently picked up a used Leer tonneau for my 01. The truck came with the factory bed liner and I'm wondering what others have done to make the tonneau rail system work. Cut the liner all around a couple inches below the top? Cut windows for the clamps and other hardware? I'd like to keep the liner as I only plan to use the tonneau in the winter.

 

Is it an over the rail bedliner?
I'd just cut holes in it for the hardware.
OR
Remove the bedliner and go with a roll-on or spray-on bedliner. You can get the Herculiner kit at almost any department or auto store. It's a 1 gallon do-it-yourself kit that costs about $100. It's not as thick or as durable as the more expensive professionally installed spray-on liners but definately worth it.

 

It's a Toyota over the rail style. I took it out to mount the tonneau hardware. I'd pretty much have to cut it all the way around below the top rail to leave it in. I may just store it and swap back and forth.


I refinished the tonneau (paint was a different color and not in great shape) with the Rustoleum spray on bed liner. That stuff is great! The finish is too rough as it comes out of the can but a little sanding after it's dry and I've got a tough, uniform, satin black tonneau for $15.