Don´t know what exactly what you want to pack up there. But with the stock roof rack, I`ve had good luck with military duffle bags (cheap at the surplus store). Clothes, boots camping gear, use garbage bags for a waterproof liner. I´ve had six up there, tied across the side rails, sitting right on the roof, with the straps and closing clip, wraped around the cross bars as insurance. Could grab the whole load and shake it, the XJ would move, tied nice and tight, a solid load.
Only problem I had was the carry straps for the duffle bags, flapped in the wind. Next time I´ll duct tape them down. I´d also probably be carefull about rubbing, possible it could damge the paint on the roof (the least of my worries). Didn´t dent anything or cause any major problems what so ever.
Used a gutter mount roof rack once, my gutter chromed covers would never stay put after that (tried bending the clips every which way). Guess it bent them just enough, they wouldn´t hold anymore. Probably should have siliconed them on, they are gone with the wind now.