I dont think it matters what position when jelqing, but the positioning of the finger and thumb when you grip may. I never used to jelq thumb on top, finger on the bottom like is standard for jelqing.
It never felt right for me, so I used to use the same grip technique - finger and thumb - but applied the pressure to the sides of the penis, alternating hands so the thumb on each hand would work the opposite side on the penis.
When doing that I could apply more pressure on the side walls, rather then the conventional jelq technique which applies force downwards.
Have a play with both methods, the conventional top to bottom, and the other variation, which just requires a slight movement of the wrist for the digits and thumb to be in place.