The legendary system is the Project Phoenix version of the epic rules. Since there are no "epic rules" as such, it's simply a ruleset that applies to levels above 20th. Very little actually changes post-20th level; attack and save bonuses continue to accrue (though see below), and you can continue to gain class levels in a base class (if the DM allows it), along with class abilities. It is fully integrated with the core rules; the only reason that it is in a separate section is so that groups who don't wish to let base classes go past 20th level or use legendary spells can safely ignore them. Monsters and magic items will be integrated into the core rules as normal; if you don't wish to use them, it's easy to ignore them.
That being said, there are a few simple rules in place to keep the system from falling apart once you get much past 20th level. These are:
Base attack bonus (and iterative attacks gained from it) is capped at +20. After that, all characters revert to the poor attack progression thereafter.
Likewise, save bonuses are capped at +12; after that, all saves revert to the good progression.
No progressions are provided for prestige classes. This is because a) they don't lend themselves well to infinite progressions; and b) I don't design PrCs to be taken past their maximum level (10th, in most cases). If you wish to extrapolate your own legendary progressions, feel free. There are a few PrCs, though, that are designed for characters over L20; they are listed below.
And that's it. Anyone who takes more than 20 levels in a base class uses the legendary progressions. They only go for another 20 levels, but you can extrapolate them easily.
Legendary Classes
Legendary Prestige Classes
Legendary Magic
Legendary Magic Overview (includes legendary spells)
Legendary Monsters
All monsters that formerly appeared in the ELH are now listed with the other monsters from the Monster Manual.