Modifying new bedliner

I just bought a new Silverado 2500HD, Crew Cab, Longbed, LS+, with 8.1L V8, 3.73 gears.

After much shopping around and comparison, I'm having a under-rails PendaLiner Bedliner installed today (have a Truxedo Lo-Profile Tonneau cover on order).

The Bedliner has access holes for the built in tiedown hooks in the corner of the bed. But, it looks like the Stake Pocket access holes will be covered up by the bedliner (I don't know what else to call them....not the 2x4 slots on top of the rails but the round holes a few down from the pockets). Since I use those holes to atttach bungee straps, I plan on cutting holes in my new Pendaliner. Anyone know of a problem in doing so?

Also, the tonneau cover is inside-the-rails roll-type. I know there are clamp/adjustable cargo cleats/tiedowns that can be attached to the bedrails that go UNDER the covers, but those are for the snap/velcro covers that attach on TOP of the rails....anyone know of similar tiedown clamps that can be used with the inboard type covers?

Thanks
Pete

you should get it rhino lined instead. then there are no holes to worry about cutting out.