An attached run is very important. Depending on your predator situation, you need a tight run. Personally, mine is totally enclosed over the top, but some get by with less.
If you are just getting started with a waterer, I would recommend the nipple waterer for the warmer months, (I can't keep mine open if the temperature gets below 10oF) However, they do keep the water cleaner than the old fashioned waterer.
Bedding, you need a good deep pile of bedding. Many people here use a poop board under the roosts. Under the roosts is where most of the manure will accumulate. A poop board under neath that can be quickly cleaned each day, keeping your bedding fresher. This is VERY important if your coop is the least bit small.
Take a look at articles on ventilation. More than likely, you need considerably more ventilation than most people think.
Personally, I try to keep good clean water, fresh feed available, and reasonably clean coop/run. I do not medicate everything, and I never treat a sick chicken, I cull them. It keeps the flock healthy. Many people on here will recommend a lot of other supplements, but I don't think they are necessary or that effective. However, it kind of depends if you are into more individual birds as pets, or into having an ongoing flock, in which the individual birds come and go.
Good luck, this is a fun hobby.
MRs K