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Help! Newbie with tank set up problem!!!

This is my first post, I've been lurking and learning thus far. I am a
little freaked. Tonight,  we are setting up the whole filtration/CO2 systems
for my new 180g Discus tank (6 x 2 x 2)...last night I filled the tank 3/4
full in preparation for tonight.  Here's what happened...naturally I had
totally landscaped the gravel, wood, and rocks before I filled the tank..it
looked wonderful!!!  I have for substrate a 2 1/2 to 3 inch layer of Profile
(the less expensive aquatic plant soil) with a couple inches of gravel over
it.  THe gravel is totally rinsed and clean, and my wood--rooty looking,
very cool, lots of it--was also conditioned in preparation.  So everything
was fine...until a couple LARGE pieces of wood (with their useless slate
bottom panels attached) popped loose and came up, floating like boats in the
harbor.  I expected this might happen, though I tried to position enough
slate around the bases to hold it down--but the pieces are big and up they
came.  Up until then the water was crystal clear....when the wood popped up,
it brought up profile and very mildly murked up the water, which I figured
would settle down overnight...but this morning the tank looks really
murky....maybe there is some tannin here also, no big deal, but it is MURKY
in there....I weighed down the offending floater wood last night so it can
start sucking up enough water to waterlog and settle down (I know it will
take a while)...it looks like real crap in there currently; when we get the
prefilter and filter, etc on tonight, will this murkiness get sucked out?  I
could dump the water and start over but that's extreme.  (Esthetics have
been known to rule me--I'm an artist...)  Anyhow, I had intended to let the
water settle in over night, get my plants into the tank before it is totally
filled and I have to put on a wet suit to work in there, and then finish
filling so tonight we can set the height for the prefilter, etc and just get
it all up and running...just tell me--is there any other reason the water
could have gone so murky besides these two variables? It looks awful.  Will
this clear with the filter on?  Clearly the woman needs reassurance...or
direction.  THank you in advance for any and all replies.