You are asking very sensible questions.
Not all of them have definite answers -- because there are many right ways to keep chickens -- but they are good questions.
Yes, I have a huge coop, 16'x16' and I do bring the gorilla cart in sometimes. It depends on what I'm doing.
I'm not a very tidy person so I tend to get messy when working in the coop. Also, I work in food service so if I'm grabbing eggs before going to work you certainly don't want me inside the coop with the poop dust flying around and getting on my uniform.
I bought a nurse's scrub jacket to use as smock sometimes when I'm collecting eggs before cooking dinner at home or otherwise needing a quick cover over something that doesn't need to get shavings stuck to it. I also have a good pair of rubber muck boots.
As for nests,
For each adult, standard-sized hen you need:
That's a matter of personal opinion and convenience. I like to have food and water in the run myself, but in the big coop I have room for it and, since with a larger flock it's good to have multiple feed and water stations, I have them both in and out.
My preference is to have the nests handy to the door and the roosts opposite. There are many possible layouts, all of which work.
I suggest you look at a bunch of coop pages and think about how you'd like or dislike working in the coops shown. Here are some links to get you started:
Medium Coops
https://www.backyardchickens.com/articles/my-barn-red-and-white-coop-complete-build-photos.75458/
https://www.backyardchickens.com/articles/my-coop.74322/
https://www.backyardchickens.com/articles/egg-song-music-factory.74019/
https://www.backyardchickens.com/articles/perkolators-modern-chicken-estate-2019.75345/
Large Coops
https://www.backyardchickens.com/articles/alaskan-woods-coop.75752/
https://www.backyardchickens.com/articles/my-coop.76267/
https://www.backyardchickens.com/articles/post-and-beam-styled-coop-run.76181/reviews
https://www.backyardchickens.com/articles/le-palais-de-poulet-the-chicken-palace.67196/
https://countryliving.blog/2021/06/15/my-coop/
Shed Conversions
https://www.backyardchickens.com/articles/the-mulligan.74743/
https://www.backyardchickens.com/articles/aarts-coop-page.65912/
https://www.backyardchickens.com/articles/the-scoop-on-a-rubbermaid-big-max-coop.76444/
https://www.backyardchickens.com/articles/toy-shed-conversion.64879/
As you see, there are many ways to manage litter. This is my article on Deep Bedding: https://www.backyardchickens.com/articles/using-deep-bedding-in-a-small-coop.76343/
If you like the Deep Bedding idea be sure to design human doors and pop doors so that the litter can pile up without spilling out.
Good advice here.
Those are the numbers I remember too.
In my smaller coop I might have to clean every 6-8 weeks. The giant coop with the active composting Deep Litter system should go along fine until I want the compost.
With Deep Bedding -- the dry system -- the poop gets mixed into the abundance of dry bedding, dries out so that it doesn't stink or grow bacteria, and is thus neutralized.
With the moist, actively-composting Deep Litter system the composting action neutralizes the poop.
Nests and roost can generally be placed for your own convenience. I put my nests at elbow height so I could gather eggs without bending because I have arthritis and have to think about that. I put my roosts at shoulder level so that I could easily take birds off the roost for exams, etc.
Here's one very simple way of setting a removable roost. The branch fits firmly against the sides of the coop:
Sometimes people put the nests under the poop board to make their coop more space-efficient. I don't like bending under the roost to get to the nests myself. It's a matter of personal preference.
Not all of them have definite answers -- because there are many right ways to keep chickens -- but they are good questions.

Exactly! I need to measure my wheelbarrow to see how wide it is. Do you ever bring yours inside?
Yes, I have a huge coop, 16'x16' and I do bring the gorilla cart in sometimes. It depends on what I'm doing.
Great point. Can quickly grab the eggs. Are you supposed to change clothes when you go inside the coop?
Also, for 12 chickens, how many nesting boxes do I want and how high should I place them?
I'm not a very tidy person so I tend to get messy when working in the coop. Also, I work in food service so if I'm grabbing eggs before going to work you certainly don't want me inside the coop with the poop dust flying around and getting on my uniform.

I bought a nurse's scrub jacket to use as smock sometimes when I'm collecting eggs before cooking dinner at home or otherwise needing a quick cover over something that doesn't need to get shavings stuck to it. I also have a good pair of rubber muck boots.
As for nests,
For each adult, standard-sized hen you need:
- 4 square feet in the coop (.37 square meters)
- 10 square feet in the run (.93 square meters),
- 1 linear foot of roost (.3 meters),
- 1/4 of a nest box,
- And 1 square foot (.09 square meters) of permanent, 24/7/365 ventilation, preferably located over the birds' heads when they're sitting on the roost.

I was thinking of keeping their food and water inside the run since it’s enclosed. That way, they sleep and lay eggs inside the coop and drink/eat outside of where they sleep/lay. What do you think about that idea?
That's a matter of personal opinion and convenience. I like to have food and water in the run myself, but in the big coop I have room for it and, since with a larger flock it's good to have multiple feed and water stations, I have them both in and out.
Also, what about setting up the inside? Do I want a table all the way around? Just a few nesting boxes, etc? Not sure how to design the inside.
My preference is to have the nests handy to the door and the roosts opposite. There are many possible layouts, all of which work.

I suggest you look at a bunch of coop pages and think about how you'd like or dislike working in the coops shown. Here are some links to get you started:
Medium Coops
https://www.backyardchickens.com/articles/my-barn-red-and-white-coop-complete-build-photos.75458/
https://www.backyardchickens.com/articles/my-coop.74322/
https://www.backyardchickens.com/articles/egg-song-music-factory.74019/
https://www.backyardchickens.com/articles/perkolators-modern-chicken-estate-2019.75345/
Large Coops
https://www.backyardchickens.com/articles/alaskan-woods-coop.75752/
https://www.backyardchickens.com/articles/my-coop.76267/
https://www.backyardchickens.com/articles/post-and-beam-styled-coop-run.76181/reviews
https://www.backyardchickens.com/articles/le-palais-de-poulet-the-chicken-palace.67196/
https://countryliving.blog/2021/06/15/my-coop/
Shed Conversions
https://www.backyardchickens.com/articles/the-mulligan.74743/
https://www.backyardchickens.com/articles/aarts-coop-page.65912/
https://www.backyardchickens.com/articles/the-scoop-on-a-rubbermaid-big-max-coop.76444/
https://www.backyardchickens.com/articles/toy-shed-conversion.64879/
Some people love to have a poop board, and they scoop the droppings every day, so their coop stays nice and clean and does not smell.
Some people prefer to have no poop board, and the droppings land in the deep bedding where the chickens scratch it all around and mix it up. More bedding is added at intervals, and every year or so the whole thing gets cleaned out. Done right, that coop doesn't smell either. This is the style I prefer.
As you see, there are many ways to manage litter. This is my article on Deep Bedding: https://www.backyardchickens.com/articles/using-deep-bedding-in-a-small-coop.76343/
If you like the Deep Bedding idea be sure to design human doors and pop doors so that the litter can pile up without spilling out.
As long as the coop does not stink and the chickens are healthy, any method you like is fine. But it is something to consider as you plan the inside of your coop.
Good advice here.
I forget the usual recommendations for spacing roosts, but the basic idea is that chickens should not bump their heads or tails on the wall, and should not peck chickens on other roosts. I'm thinking about a foot from the wall and about two feet between roosts, but I may be off a bit there.
Those are the numbers I remember too.
Wait, with deep bedding, you only have to clean it out once a year! Won't they be walking around in poop all the time?
In my smaller coop I might have to clean every 6-8 weeks. The giant coop with the active composting Deep Litter system should go along fine until I want the compost.

With Deep Bedding -- the dry system -- the poop gets mixed into the abundance of dry bedding, dries out so that it doesn't stink or grow bacteria, and is thus neutralized.
With the moist, actively-composting Deep Litter system the composting action neutralizes the poop.
How high do you recommend putting the roost? As far as the windows, what size do you recommend? Do you recommend buying them locally, or is there a website that allot of BYC users use?
Nests and roost can generally be placed for your own convenience. I put my nests at elbow height so I could gather eggs without bending because I have arthritis and have to think about that. I put my roosts at shoulder level so that I could easily take birds off the roost for exams, etc.
Here's one very simple way of setting a removable roost. The branch fits firmly against the sides of the coop:
Would I want the nesting boxes under the roost or on an opposite wall?
Sometimes people put the nests under the poop board to make their coop more space-efficient. I don't like bending under the roost to get to the nests myself. It's a matter of personal preference.