There are a few ways to clarify your beer; during brewing, chilling, after fermentation, and in the bottle.
When brewing, adding some Irish Moss helps with clarity. It grabs the proteins and clears up the brew.
Getting the wort down temp quick also helps (using an immersion chiller, etc), from what I have read.
If the brew is too cloudy for your tastes when in the fermenter, before bottling add some gelatin. Search the forum and online on how to do this, involves cooling the beer and adding gelatin for 24 hours.
As far as it being cloudy in the bottle, once carbonation is set then chill the beer good. In cold temps the yeast especially, but also other floaty bits, will tend to drop to the bottom of the bottle. Just pour carefully and leave the chunks in the bottle.
Cheers!