Not knowing what type of skimmer you have makes it a little difficult to really give advice. Set it so you get bubbles coming up but not into the cup. Let it run for a day and see if you get bubbles coming up into the cup. You should get a thick green/brown slimate and very little water. Lower the skimmer if you need to pull more and raise if you need it dryer. I wouldn't run it while running in the tank. All that gunk will help cycle the tank.
Going into the sump or in the tank? With a sump mount make sure it's in a portion of the sump where the water level remains constant. Then the same rules should apply. I'm not familiar with that skimmer so maybe someone who has one can be a little more helpful.
Still the same advice. You let it run awhile then adjust it up or down to get the best skimate. Each time you adjust the height let it run for a while because it often takes a while for the oils to build up in the skimmer. Some of us like a drier skim while others prefer a higher volume removed from the tank. That's your choice but I prefer not to have to empty it daily or strip too much out of the water so I like it drier.