Depends entirely on the piece. Showerheads typically, same rule as trees. Honeycombs (which I prefer a domed one, to flat) usually, just the water covering the perc will work... though, with multi level percs, it gets a bit more complicated. DGs I'm pretty sure, from a vapor standpoint, I've seen the levels jut below the perc.
Most pieces I own, are water levels, just above the highest level of the perc. Not all of them need to be run that way. Especially pieces like the Big Mona and to some degree, the DR. As you start your pull on all pieces, this will increase air pressure, raising the water level... typically, then utilizing the upper level perc. Some piece, especially smaller vapor pieces, don't have enough wiggle room... or just aren't designed to raise the level like that. With Big Mona, I can drop the water down almost half-way down the perc, but when I start the pull, it pushes the water level up over the perc.