So you are northeast of Sacramento. You can get pretty hot in summer but probably don't see freezing weather or snow that often. That helps. Yours can at least get outside practically all day every day.
I don't see any physical dimensions on that coop or run. Do you have a link to a site that gives those plus photos of inside? That could help making specific suggestions. In general I don't much like those prefab coops either but a lot of people use them. They often have to make modifications. What I'm looking for are dimensions in feet or inches and the interior layout. Especially roosts and nests. Does it come with a tray for clean out?
Do you use hay or pine shavings for the floor, how often do you clean, what type of waters and feeders do you use.
We all do these things differently. There is no one way that is right for everyone or wrong for everyone. With a small elevated coop like that popular choices are pine or aspen wood shavings, hay, straw, grass clippings, sand, or dried leaves. My thoughts on bedding is that they should be available and relatively inexpensive. Everyone has their own favorite but the strange thing is that different people have different favorites. I knew of one lady on the Gulf Coast that used Spanish moss.
How often to clean? Depends on how often you need to. I use my nose to tell me when I waited too long. In a small coop like that with five chickens you may be doing poop management on a daily basis. That doesn't mean you need a daily deep cleaning or changing out bedding. Some people change bedding weekly, some go a lot longer. It depends on your poop management and how dry the coop is.
As for feeders and waterers, there are all kinds. Some of us make our own, others buy one of the many different offerings. With that small coop you probably will not be able to feed and water inside. Feed needs to stay dry so you may need to hang a feeder under the coop. I personally don't worry too much when it rains in the waterer.
How will they know to go back in their coop at night?
Instinct. You may have to train them to sleep inside but once they get in the habit of sleeping inside they instinctively go there each night at dark.
