i had that happen to mine. i got this thick film of sludge on the top of the water and the smell was absolutely horrible. it took about 2 weeks for it to go away.
there's a product called Stability which is very high in the oxidisers for ammonia, nitrites and nitrates. this product claims to be able to let you put fish in from day one as long as you follow the instructions.
after my use with it i trust it but not enough to not cycle a tank first. i would most certainly use it to speed the cycle up though.
you'd be well advised to swap the pre-filter pads over regularly and once the smell goes you might want to add some activated carbon to clear the water up, but i would only do that at the tail end of things as the filtering will take care of a lot of the brown.
if you can get Stability then certainly start using it for my money. its worth every cent.