Preference points are for the elk, deer and elk/deer combination licenses that include a general season tag for those species.  Preference points don't give you chances, they put you in a group ahead of other hunters.  More points, closer to the front of the line.  Bonus points don't apply here.
Bonus points are for special tags like moose, sheep, goat, and the limited entry deer and elk tags.  Bonus points give you more chances in the special draw.  Preference points have nothing to do with this part of the draw.  
If all you want is a general tag, you only apply for that and burn your preference points.  
If you want to apply for a limited  entry tag as well, you apply for the deer, elk, or deer/elk combination license as above, and on the same form you also mark down which limited entry permit you want to try for and your bonus points come into play in this second part of the draw.  
If you are unsuccessful for the general tag, you obviously don't get the LE tag and get to hunt some other state.  If you are successful for the general tag, you may or may not get the LE tag, but you still get to hunt any open general unit.  
Jeremy