You'll get a rank smell during the cycle. IMO it's more like a dirty toilet for the first couple weeks particularly. It'll shift through the second phase, and after the cycle it'll smell like rich black soil.
If you don't have any lights like I described, you could get one of the cheap lower quality CFLs to do the same thing, but it's not that necessary. Just try to stand with your back to the whitest light source you can get and that should be sufficient. Take the shade off a bright lamp, for example. Try different rooms (wall, ceiling, and floor color can have a major effect on light quality, distorting colors) and lights until you find one you're comfortable with - once you're used to reading under a certain light, being able to accurately see the color is less important than being able to consistently see it. Yellow may look green in a certain room, but you'll get used to the "right" shade of green and still should be able to pick out bad readings.
Using bottled water, you should post in tropical discussion for some more experienced help. Bottled water comes lacks the trace minerals fish need and has very low to no hardness, making the pH very unstable. You'll probably have to add something to the water to make it suitable. There are some products like this, somebody can probably advise you. If the water's coming out brown, that's probably iron pipes rusting, some old water systems in my state have iron mains and the water is unfit for much of anything. If possible, it may be worth having a plumber look at it (in case you have iron pipes yourself), and if it's definitely from the water system, complain to local authorities about the state of the water supply (which likely won't do good unless you can organize other affected households, but complaining has beneficial and stress relieving effects
)