I've cut a lot of dovetails with the LS system. I first cut the thickness of the workpieces to approximately the suggested thinknes shown for the selected bit and template. Then I adjust the height of the bit to match as closely as I can the thickness of the workpieces.
Next I make the first cut for the tail cuts and then move the fence to the second tail cut mark and cut that second cut, and after doing that I check the fit and tweak the height of the bit as needed to get the proper fit. All of this of course is done after going throught centering drill.
Once the height of the bit has been adjusted so that the fit is right I do one other thing when cutting the pins if the workpieces are very hard.
I widen each cut just slightly by doing the following. After making the first pass on each of the pin cuts, I advance the fence by five clicks and make a second pass, then back the fence back by ten clicks, make the third pass and before moving on to the next cut return the fence to it's original position by moving the fence forward five clicks. This is a little extra effort, but it often makes the assembly much easier for me. Hope this helps.