Probably more down to personal preference, I have them set with eye just lifted slightly off the bottom (using a D Rig, or Hook Ring Swivel and Bead set near the eye), as the bait causes the eye to be lighter therefore the hook point is heavier, which in turn makes the hook sit in the optimum hook position when the bait is sucked in.
Thats how it goes in my head anyway , Im sure others will have there own favoured method for presenting this type of bait but this mine.