The libraries are split up approximately by usage. Each one is included by group and name, so to include y_va, which is in Coding use:
#include <YSI_Coding\y_va>Although YSI provides a lot of libraries, they aren't included unless you include them. So if you don't want y_zonepulse just don't include it and it won't appear in your mode at all. This means YSI can contain a lot of functions, but they're all optional.
PAWN scripting improvements (i.e. new language features).
Core libraries, used almost everywhere else.
Data structures and algorithms.
Optional features.
Libraries that provide information about the game.
Libraries for managing players.
Libraries for controlling the server.
Libraries for interacting with persistent data.
Libraries that have in-game visible effects.
No-one actually knows! The original idea was "Y_Less' Server Includes", but "Script" and "Server" were frequently intermixed, and there are more devs than just Y_Less now, so the "Y" just became a recursive acronym for "YSI". There are now several official meanings, each incorporating different aspects of YSI:
Core libraries.
Coding libraries (pawn language extensions).
Game related stuff (commands, properties, text etc).
Extras, like login and commands.
The macros (though in their defense, writing macros to do the parsing within the compiler limitations is VERY hard).
y_tho.