The super meter works much like you would expect in any other fighter, with its own twist. You build meter for hitting opponent, having attacks blocked, and whiffing special moves. You also get meter from getting hit or blocking attacks.
In KOF XIII when you are at your first character you can store up to 3 stocks. Your second character can store up to 4 stocks, and your third character can store up to the maximum of 5 stocks.
Every Desperation Move (Chinese for Super) costs one stock. Every EX move, unlike 3s and SF4 but similar to Vampire Savior, also take one full stock. Super Desperation Moves are stronger versions of Desperation Moves and will take two stocks. Neomaxes are devestating super moves that take three whole stocks (in addition to 100% of your HD gauge) of your super meter.
The gauge is also used for two special techniques known as Guard Cancel Roll and Guard Cancel Blowback which both take 1 gauge to execute.