The beer will clear on it's own in 3-5 days in the bottle. After 2-3 weeks the sediment will be compacted and shouldn't lift off the bottom of the bottle in the first pour (or two), you just have to be careful pouring the last bit and stop as soon as you see sediment floating towards the mouth.
BUT.... If you chill it in the fridge down below about 10C, the cold break material will clump up in solution and the beer will become cloudy again. This is "Chill haze".
You can lager (or cold store) the beer in the fridge for 3 - 5 days to allow the chill haze to settle out naturally (I've never tried), or... you could read this:
http://www.byo.com/stories/techniques/a ... chill-haze
If you read that carefully you'll find that things like Irish Moss and Protofloc are really meant to stay in the kettle. The protiens and what not that are in the hot wort clump up when the wort is cooled. If you simply syphon all that into the FV, along with the irish moss or protofloc then you have effectly achieved nothing with them. The beer will still take 3-5 days to clear and will still go cloudy when chilled.
The idea is to let the wort sit _with the lid on_ after cooling for a few hours, for the cold break material to clump onto the protofloc/irish moss and fall out of suspension to the bottom. You then syphon from the top down, leaving all the cold break material at the bottom of the kettle.
Then when you chill it down, you should not get much, if any chill haze.
Sounds easy, but I've only just learnt this myself.
Out of interest, I have found that syphoning the cold break material and protofloc into the FV has resulted in several of my beers developing the habbit of sediment floating up to the surface after the first pour. I don't know if it's related, or just those beers for whatever reason.