Welcome to BYC.
I suggest, if you haven't already, to use the search function at the top of the page and type search for 'coop', 'design', etc. and you'll find hours of reading that will help you.
My biggest suggestion is to build BIGGER!! I've never (literally never) heard someone say, "well, darn, we sure built too big of a coop!"
Some of the building is personal preference or done according to where you live - a hot vs. cold climate.
I built (well, my DH and sons built it - sweet guys) my hen house so I could walk inside a 'people' side to get to the nest boxes. I didn't want my children or I to have to stand outside in freezing blizzards or pouring rain to collect eggs. Also, since my children have been known to leave the nest box doors open this way the chickens can only get to the people side and they are still safe inside the enclosed hen house. If the collection doors opened to the outside my hens would be able to get outside when we are not here and predators could get inside.
I also love being able to walk inside my coop. Some people like smaller, shorter coops and build them up off the ground so they don't have to lean over to clean them out.
Use the best wire you can afford for their run area. Build it as predator proof as possible from day one -- it's heartbreaking to lose a chicken(s). Hardware cloth is always the best option but also very expensive. The next best option would be welded wire with 1" inch chicken wire wrapped around the bottom up about two feet and buried into the ground at least 15-18 inches.
If you can afford it go with a cement floor. Next option would be a solid wood floor (IMO covered with linoleum).
Hope some of this helps. Have fun and good luck!