Some of the extra steps you are being asked to do is to negate Steams protections against patched execute files. Essentially when you are modding a game you are asking it to access files that it would not normally look at. Simple mods like adding a new texture to an item you will turn on a option called “archive invalidated” that tells the main execute file (the one that loads the game) to check if there is a file with the same name that is not IN the archive (BSA in Bethesda’s case).
The issue is that as you are slightly altering and telling the execute file to do that can cause Steam to suspect that you have a “cracked” or stolen copy. The Mod Manager sidesteps this ( it does not however bypass any copy protection)
The Script Extender is useful for advanced mods which alter the coding of the Game engine (Creation engine is what Skyrim runs on, its a heavily modded version of the Gamebryo engine which most Bethesda games are built with)
What this allows is the addition of commands and complex scripts that the game engine is not programmed to do, to put it simply, When Bethesda designed the game they had no need to have the game to understand tidal patterns of the sea. So they did not programme in any commands into the engine to understand how some land will be covered by water at some points of the day and not others. The script extender allows a modder to code that into the game. There are dozens of things that the SKSE can be used for and modders will take full advantage of them.
A mod sorter is used to put your mods in order so they do not conflict with each other. in your “Load Order”, this is your list of mods that you are running in game, Some people will be running over 200 mods at any one time on a game as vast as Skyrim. This obviously can cause conflicts, you have one mods telling the game to do one thing while another mod is telling it to do something else. The game engine automatically gives priority to the mod that was loaded higher in the order, It cancels out the other change, the problem comes when it does the wrong thing and either crashes the game or breaks the game because something that should be there but is not. The classic example would be two different modders altered the area around a town, both slightly moved the same rock to put in something. When you load your game with both mods, your game does not know which rock movement is right and because it can not place the rock into the game world when it knows it has to, it crashes the game. A bad load order is a nightmare. The mod sorter is therefore your best friend.
The patch for the main game is .INI tweaks, a .INI file is basically the info file that your computer is using as rules for the game engine. The tweaks it involves is telling your computer to use more of the computers RAM than the game was designed to. When you play a game it preloads many elements so the game is faster. On Fallout 3 Bethesda designed the game to use 1GB of RAM to preload elements. This is plenty when you look at what the game needs to run. However when you start using mods the files may be much much larger, so you run out of memory when playing the game, this either crashes the game or it runs slowly.
Tweaking the .INI allows you to tell the computer to use 4GB instead. This allows these much larger files to be loaded. The unmodded game looks fantastic but uses small image files to boost performance, many modders will upgrade these image files to be in HD, and therefore much larger files. These “Texture Packs” can be gigabytes in size so unlocking the extra RAM is very helpful in maintaining the performance of the game.
You can also adjust the .INI to allow Multiple Threads, what this means is telling the computer to use all the power of your processor instead of pushing all the game data through one part, this can increase performance overall.
It can be daunting when you get started as it does appear very complex but Bethesda games have a very active modding community. Bethesda releases kits for the modders to use to mod the game easily and has done for years. Due to this whenever they release a game there are dozens of modders upgrading the game and fixing issues they find. Many of the programs you are being asked to instal are the end result of years of work by modders. The Mod Manager for example combines almost a dozen smaller programs that used to be used to make mods work. Some talented people got together and put them altogether and allow the masses to get the full potential out of the mods available. It is very useful for turning on and off mods easily instead of having to manual delete all the files connected to it,
Im very tired but i hope that made some kind of sense.