I'm assuming you are cycling with fish already in the tank as you are doing daily water changes?
If ammonia is staying at 0 and nitrite is staying at zero, you are cycled.
Keep an eye on the levels for a while. If either ammonia or nitrite creep up above zero do a water change, other than that you can just do weekly water changes of around 25 per cent. (depending on your stocking load you may have to do more or could do less).
Nitrate of 5 is no problem to fish at all. Nitrate will build up over the week but will then be removed through your regular water changes. It's rare for nitrates to harm fish (though some species are sensitive to it). There are even some threads around showing research that nitrates of up to 400ppm don't harm fish.
As for the yellow water.. do you have any bogwood in the tank? Bogwood can leach tanins into the water turning it yellow. It's harmless to fish but a lot of people don't like the look of it. To avoid it, soak the bogwood in a bucket of water for a couple of weeks.
The smell is a bit more worrying. A healthy tank shouldn't smell bad. Could you describe it all?
Brown filter media isn't a problem but if it is clogging up your filter and reducing the flow, next water change take the media out and give a bit of of a swish in a bucket of tank water to clean it a bit. Don't use tap water on it (that will kill the bacteria) and don't scrub it or anything. Probably best only to do a bit at a time (if you have multiple sponges).
What size is your tank and how many (and what type) of fish do you have?