Ok, I am going to attempt to answer all of your questions one at a time.
First of all, you wondered about clothing and arming your dwarves. While is does become a problem at some point, it doesn't usually for a while, you have at least enough time to buy cloth from the merchants (they always come with a ton) and build a couple workshops. Arms-wise, you should only have weapons in use by your military, and you shouldn't need a ton of military dwarves, it is always most efficient to have your defenses based around traps.
Secondly: bedrooms. I have found that it is best (until you reach the population cap, although that tends to be a bit buggy) to have all of your dwarves sleep in one giant dormitory with many beds. You can do this by building a bedroom that encompasses all of the beds in the area and then toggling "dormitory" to "Y." This way, you have one area where all of your dwarves sleep, and the only thing you will need to worry about is having enough beds. You probably only need the number of beds to be 25% of the number of dwarves you have, as that should cover all the sleeping dwarves. It is even better to have a much larger room with half of it being a statue garden, as then you will have dwarves in the room who are awake and will see it if any vampires start killing dwarves.
For pens and pastures, there isn't a great way to make them efficient that I have found. There isn't really a great need to have them, though, because you can buy a lot of cheese and cloth from merchants. The only reason you would need a pasture, I've found, is for a chicken egg-laying area, but for that, you can make it underground in stone, you just need to be sure to have nest-boxes.
Building configuration-wise, I find that it is good to have a set plan for design before-hand. For example, know that you will put a lot of your workshops in one area, and your meeting hall and bedroom (see above) in another. It's also good practice to only dig out enough room for the workshop and not to group them all together in one room. You should also have rooms for your stockpiles near the corresponding workshops. Also be sure to have one "main" hallway, it should be 3-wide or more, as this will prevent traffic jams down the road.
Finally: farms. I would recommend you build a couple plump-helmet farms, as large as possible, to feed your dwarves. Seeds shouldn't be a problem, just go to the overview (z) menu, move over to kitchen, and disable plump helmets for cooking but not for brewing. You should have several breweries to make alcohol, and these will also return seeds. It is also good to have an egg-laying center (see above) and a kitchen. Hens and roosters will produce a ton of eggs, and if you set your kitchen to auto-repeat cooking easy meals, you should be able to feed your dwarves.
Best Answer
When you embark on a new fortress, you have the option of choosing the size of the embarkment area for your new fortress. This size, which usually defaults to 4x4, is the size on the large world map which your fortress will occupy. Outside this area, the rest of the world still exists - migrants1, diplomats, nobles and goblin sieges all must come from valid civilizations that exists elsewhere. History still moves on, and occasionally you get hints of that, such as when Ages change.
From your perspective, however, the new playing field will be all that you have - there is no way of commanding dwarfs to move outside this zone, nor to expand the zone once you start a game. You will have to make do with the resources you can find in this area. To get more, you can trade with caravans that comes once in a while, or strip them off dead enemies that attack your fortress. Anything that moves out of the zone, like liquids that flow outside the zone, items stolen by animals, children kidnapped by Kobold thief, etc., will be considered outside the simulation as far as the game is concerned.
You might think this zone is small, but remember that the world in Dwarf Fortress is three dimensional. The world extends hundreds of levels downwards, and you should have no shortage of space once you start excavating. To really see the "world", you have to play Dwarf Fortress in Adventurer mode, though this is not possible while there is a Fortress still being played in the same world.
1 The only exception here is that first two waves of migrants are coded such that they will always arrive, regardless of the size of your parent civillization.