Are you wondering about the clarity of the beer? If so there are a few thing to help with getting clearer beer (mostly it's an issue of appearance, though in some cases it can lead to flavors that you may not want in certain styles):
Make sure to have a get a really vigorous boil during your brew, and chill it as quickly as possible afterwards to yeast-pitching temperature. At the 15-minute mark for your end of boil you can toss in a teaspoon of Irish Moss which should help, too. But yeah, I suppose you should find more trub at the bottom of your fermentor... you're introducing the possibility for more particulate matter with AG brewing vs. extract. I could be wrong about that though.