Mostly palms down, but I vary my grip sometimes depending on what I'm aiming for. Another thing to think about; some guys, myself at the beginning too, would create a...."choke point" when jelqing that would produce a single, fluid-filled bubble. A much smaller version of "the donut effect". Almost like a blood-blister but just plain fluid inside.
If you think of the point where your thumb and forefinger come together as an hour hand on a clock, then changing what time it points to can help avoid the creation of the fluid ponds.