Also, keep in mind that "Season" folders (erroneously, to my eyes) don't really exist for the scraper's purpose as folders but as a way to figure out the episode itself.
That is, you can put a thumb to the tv show or a thumb to the season but the scraper won't understand the tv show contains "seasons". This whole arrangement, to me, could be improved. But the amount of changes required to create a "season" entity in file mode (it exists, virtually, in "Library mode") is unmanageable.
Anyway, to answer your question: What you're being redirected to is the XBMC wiki pages, the manuals. No the FAQ for the MacOS version but the document for the whole of XBMC.
You can ask for things here and more often than not you'll get some sort of response but it is expected that the user has actually tried to look for the documentation of XBMC.
A whole different issue is that the XBMC team is still learning what it means to deal with non-technically-savvy end-users, which is obvious in some of the responses that can be seen around here sometimes (less now than before, so I guess the "End User" part of the forum topic has finally permeated).
Now, if I can see your questions correctly:
1.-Scrapers and lookups:
You should separate the folders you have for Movies than those you have for TV Shows. You should also create folders for movies when more than one file is involved (for example, one AVI and one SRT file, or a CD1 and a CD2).
For TV Shows XBMC currently expects season and episode to be in the name in a familiar format (S01E12, 1x12, etc) and containing folders to have the name of the show.
Now. When you have your whole thing ordered you can go to your "TV Shows" (or "TV Shows - Fiction" or "TV Shows - English", whatever) and press "C" (contextual menu, also right button on mouse) and select "Set Content". Here you'll tell it the folder contains items of type "TV" and select one of the scrapers (I use TheTVDB) and there might even be scraper options. This will in turn start a session of scraping that depending on the size of your library (in number of items) and settings (extra data for shows and cast, download of thumbnails, etc.) might take some time.
For Folders that contain movies it's pretty much the same but the scraper would be "IMDB" (for me, at least).
When the scraper has finished you should have a folder full of items with thumbnails (poster thumbnails for movies, wide banners for tv show folders) and if you select any movie or tv show and press "i" (or select "Show Information" from the "C"ontextual Menu) you would see additional information about the item (like the description, cast, etc.).
This is my current directory structure, with comments with //:
-Movies ES // Movies in spanish language, dubbed or native - No automatic thumb
-- Spanish Movie AVI 1 // Spanish movie in Spanish
-- Movie in spanish AVI 2 // Movie dubbed into Spanish
-- MKV with Spanish Track 3 // MKV with a Spanish-Language track, no subs
-Movies SUB // Subtitled Movies - No automatic thumb
-- Subtitled Movie Folder 1 // Folder with .AVI and .SRT files.
-- Subtitled Movie MKV // MKV with Subtitles track
-- Subtitles Movie AVI // AVI with Subtitles track
-- ISO File // ISO of subtitled movie, DVD or VCD
-- DVD Movie Folder // TS_Folder from DVD with VOB, IFO, etc.
-- Movies UNSUB // Movies without subtitles or dub
-- Movie AVI // Single-File Movie
-- Movie Folder // Mutliple-file Movie
-- TV Shows // Currently watching TV Shows
-- TV Show 1 // TV Show Folder ("Smallville", "Psych", "BattleStar Galactica", etc.)
-- TV Show 1x // Season 1 for TV Show
TV Show - Episode Title - 1x01.avi // Single Episode AVI with name
TV Show - Episode Title - 1x01.srt // Subtitle for episode above
-- TV Show 2x // Season 2 for TV Show
...
-- OLDTV // TV Folder with Old TV Shows ("Automan", "Max Headroom", etc.)
...
When the script finishes scraping I end up with no thumbnails in the main folders (OLDTV, UNSUB, etc.), thumbnail in every level below that (single movie folders, single show folders) and possibly thumbnails in the individual tv episodes.
Then, if you're so inclined, you can go into specific items and press "i" to see the information (or "refresh" it if it's wrong, to select from a list the correct option) and also change the thumbnail to another one (it'll download the different available thumbs so you can pick the one you prefer).
When this is all finished you might end up with some items without thumbnail for whatever reason. This is where you can put these thumbnails by hand using jpg files named as the items and put in the same paths. These are picked automatically.
In the end this structure works for me. Feel free to ask for more info. In a civil manner, if at all possible.
2.-There's not a single skin repository nor is there supposed to be. You can download individual skins from their developers, which are not part of the XBMC team nor are they expected to be. Popular skins are xTV, MC360 and Aeon. These all have their pros and cons but the biggest con they all have is that they're never as up-to-date as the official skin: Project Mayhem III (PM3, for short).
This is this way --and you need to keep this always present in your head before you rant about the program, team or documentation--, because XBMC is still a work in progress and hasn't been finished. It costs nothing and is not supposed to be used heavily by non-technical users so the documentation still hasn't been made for this specific public. When its features are frozen and an official release is made I'm sure this information and documentation will appear, but not before then.
You can, nonetheless, help by producing documentation for end-users which, as you might have noticed, is one of the biggest holes in the project.