What is the proper way to align the headlight on a FatBoy?  Mine seams to not be lighting up whats in front of me like it should.

Line up the headlight in your darkened garage. Picture an imaginary line 4' off the floor and align your low beams slightly lower than that line. This will keep the low beam light from shining in the eyes of the vehicle ahead.

It's actually pretty straight forward.  This is from the Harley Service manual...

1. Place the bike on a level service with a flat wall 25' from where the front tire touches the ground (make sure the bike is lined up 90° to the wall)
2. Draw a vertical line on the wall lined up dead center with the bike
3. Measure the distance from the ground to the center of the headlight with the bike straight up an down and a riders weight on the seat and draw a horizonal line on the wall at this height.  This will make a cross with the vertical line you drew.
4. Turn on the headlight and using the two spring loaded screws at the top and right side of the headlight to align the headlight "hot spot" directly on the cross you drew on the wall.

It should go without saying, but this is much easier to do in the dark!

You can adjust the passing lamps pretty much the same way.  They should align along the same horizonal line and just to the right and left of the headlight spot.

To adjust the passing lamps you need to remove the blinker from under them and loosen the retaining nut that was covered by the blinker.

Note: it is easier to see the passing lamps one at a time without the headlight.  I put a hat over the headlight and one passing lamp to see just the one I am working with.

That is the manual's way of adjusting the passing lamps.  I actually run mine to where they hit at about 2 feet from the ground at 25 feet.  I like to light up the road in front of me.

Good point on using the passing lights to light up the road in front of you, the new headlights provide plenty of down-road light. I also turn my right passing light just a bit more to the right so that I can see the side of the road a little better and know if something is about to jump or run out in front of me.