Truxedo lo pro q/t cover. Mounts to the inside of the bed, not the top of the rail. When you buy it, get the one that mounts with the rail system. This cover leaves the holes in the rail 100% free for ladder racks.
It's doable. Depending on your cover, you'll probably be limited to certain ladder rack options. I have a TruckCovers USA retractable and they do make a few ladder racks that will work without modifications to the Tonneau or rack. Rack-it is one of the companies and I can't recall the other at the moment...
However, if you haven't bought the cover or rack yet, call the tonneau companies and get their input. They'll know, or should know what combos will work. TCUSA might recommend a different cover to provide more space in the bed to fit a rack.
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