autorun.inf and dstwo.ico go on the root folder. After you add these files the next time you put your microSD into your computer it will always show up as Supercard DSTWO with a supercard logo for easy identification.
Plugins, homebrew games, and emulators all come in the same format. To install them you copy the 3 files that make up a plugin (.NDS .INI .BMP) to the /_dstwoplug folder. There is no install all at once option, you pick and choose which plugins/homebrew games/emulators you want for your custom DSTWO. If there are more than 3 files follow the readme.txt to know what to do with them.
Emulators also contains tools for ROMs and emulators of different types. Also some tools for specific games.
Skins and skinning tools has a nice readme to tell you what to do.
Game guides are installed by renaming the text file to the name of the corresponding .NDS game file. Game saves are installed by renaming the save file to the exact name as the NDS file as well. e.g. Pokemon Black Version 2 (DSi Enhanced).sav for Pokemon Black Version 2 (DSi Enhanced).nds
or
Pokemon Black Version 2 (DSi Enhanced).txt for Pokemon Black Version 2 (DSi Enhanced).nds
You can view the readme in the game guide database for info on how to put multiple text files/images on one game for the game guide function.
Extra tools contains a lot of different content.
The SC2 Cheat database goes in the /_dstwo folder.
The latest kernel and kernel patch go on your microSD if you have not installed them already. The latest firmware needs to be run once if you are not on the latest firmware already. The only way to tell is to extract the update file onto the root of your microSD, and once you reach the plugin menu on your card, it will ask you to update if you're not on the latest firmware already.
Most everything else in extra tools is run on your PC, and not put on the microSD card. In general just follow the readme's to know what to do with the files. If you do not know what something is it's very unlikely that you need it.